From 4e77fa4e87c91f6696533e8e2184c1d20b3a2aee Mon Sep 17 00:00:00 2001 From: mencian Date: Tue, 7 May 2024 11:36:17 -0500 Subject: [PATCH 01/81] Revert to medium linux-aarch64 resource_class --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 342c7b19e05b55..7020f97145379a 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -9,7 +9,7 @@ executors: linux-aarch64: machine: image: ubuntu-2204:current - resource_class: arm.large + resource_class: arm.medium jobs: # a basic unit of work in a run build_and_test: From 92334436dae1338489ee84dbc18e2934c3ace4dd Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 May 2024 12:40:40 -0400 Subject: [PATCH 02/81] Update snakemake-executor-plugin-googlebatch to 0.4.0 (#47735) --- recipes/snakemake-executor-plugin-googlebatch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml index 4383f0b34e857e..e47a6fbc91962e 100644 --- a/recipes/snakemake-executor-plugin-googlebatch/meta.yaml +++ b/recipes/snakemake-executor-plugin-googlebatch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-googlebatch" %} -{% set version = "0.3.3" %} +{% set version = "0.4.0" %} # Upon version update, requirements have to be checked! package: @@ -8,7 +8,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_googlebatch-{{ version }}.tar.gz - sha256: fbc3f3dad6fca51f9d65cd66a6a1272b056213ed3ab03759523f27590c58bcd8 + sha256: ad1ebf74d6558bc5ea9d1849570fb3c5991413265c771d944e99aeb8c49217d2 build: noarch: python From c89961a97608f40566392d53d90051f75ebf5ca6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 May 2024 13:38:47 -0400 Subject: [PATCH 03/81] Update tadrep to 0.9.2 (#47724) * Update tadrep to 0.9.2 * add run_exports --------- Co-authored-by: mencian --- recipes/tadrep/meta.yaml | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/recipes/tadrep/meta.yaml b/recipes/tadrep/meta.yaml index 859bc2d118598e..d88f8af6645d09 100644 --- a/recipes/tadrep/meta.yaml +++ b/recipes/tadrep/meta.yaml @@ -1,19 +1,22 @@ -{% set version = "0.9.1" %} +{% set name = "tadrep" %} +{% set version = "0.9.2" %} package: - name: tadrep - version: '{{ version }}' + name: {{ name }} + version: {{ version }} source: url: https://github.com/oschwengers/tadrep/archive/v{{ version }}.tar.gz - sha256: 'd09bcff6c295bc5532573696db4ad15f00364f8c8dc53d3907d573be56c8011b' + sha256: '53866c0b538f1dc85dc976527127a1564586925953930b30368175c9873936ba' build: - noarch: generic + noarch: python number: 0 - script: python -m pip install --no-deps --ignore-installed . + script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv entry_points: - tadrep = tadrep.main:main + run_exports: + - {{ pin_subpackage('tadrep', max_pin="x.x") }} requirements: host: @@ -37,12 +40,13 @@ test: - tadrep --help about: - home: https://github.com/oschwengers/tadrep - license: GPL-3.0-only - license_family: GPL + home: "https://github.com/oschwengers/tadrep" + license: "GPL-3.0-or-later" + license_family: GPL3 license_file: LICENSE - summary: Targeted Detection and Reconstruction of Plasmids. - dev_url: https://github.com/oschwengers/tadrep + summary: 'TaDRep: Targeted Detection and Reconstruction of Plasmids' + dev_url: "https://github.com/oschwengers/tadrep" + doc_url: "https://github.com/oschwengers/tadrep/blob/main/README.md" extra: recipe-maintainers: From 7f2b42e3a33cad946d779e06ceb141197262ce55 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 May 2024 13:39:13 -0400 Subject: [PATCH 04/81] Update trust4 to 1.1.1 (#47742) --- recipes/trust4/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/trust4/meta.yaml b/recipes/trust4/meta.yaml index 476da155b5c9f2..97f07b02111e88 100644 --- a/recipes/trust4/meta.yaml +++ b/recipes/trust4/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.1.0" %} +{% set version = "1.1.1" %} package: name: trust4 @@ -11,7 +11,7 @@ build: source: url: https://github.com/liulab-dfci/TRUST4/archive/v{{ version }}.tar.gz - sha256: dfb08a2d08badad0d865917d0b034a5bc8db089627157a02b335c28a9500b5ef + sha256: 65ea98d468a2921c1591120041c3ca1caac76c37bd804b0d4b64b11c73a382ed requirements: build: From ce83ea0886d55e237869060ed04701477a052cb8 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Tue, 7 May 2024 23:38:17 +0200 Subject: [PATCH 05/81] [biobb_pytorch] update 4.1.3 (#47748) --- recipes/biobb_pytorch/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/biobb_pytorch/meta.yaml b/recipes/biobb_pytorch/meta.yaml index ef1fa74aef943f..4d0697eeb84791 100644 --- a/recipes/biobb_pytorch/meta.yaml +++ b/recipes/biobb_pytorch/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_pytorch" %} -{% set version = "4.1.2" %} +{% set version = "4.1.3" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 2beb946b85e02f5907caf32a08bf38230d7dd1820a16416c08546118e423b268 + sha256: 5ffce86986e458cc62f2f3695b58095d33636e35d8a29f8bc14a3c2ed1796061 build: number: 0 From e4aa8aaf609537830f9a5dd6525da51b2490f07b Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 May 2024 20:18:44 -0400 Subject: [PATCH 06/81] Update phyloacc to 2.3.2 (#47746) --- recipes/phyloacc/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/phyloacc/meta.yaml b/recipes/phyloacc/meta.yaml index 9468c7e2c2a16b..f208151958b380 100644 --- a/recipes/phyloacc/meta.yaml +++ b/recipes/phyloacc/meta.yaml @@ -1,6 +1,6 @@ {% set name = "PhyloAcc" %} -{% set version = "2.3.1" %} -{% set sha256 = "f22dfff721a788b117bb097370402aad0d1a22fb26fec9c6082eb1eb620a553f" %} +{% set version = "2.3.2" %} +{% set sha256 = "552f982801be6b1df73a330106136ba970f2bbd53b8a5eff99c3f01160dfcd7f" %} package: name: {{ name|lower }} @@ -11,7 +11,7 @@ source: sha256: {{ sha256 }} build: - number: 1 + number: 0 skip: True # [py < 38] run_exports: - {{ pin_subpackage('phyloacc', max_pin="x") }} From 2e38e50d0398d73848af5db8b6681b94d6af5ddb Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 May 2024 20:26:59 -0400 Subject: [PATCH 07/81] Update snakemake-executor-plugin-slurm to 0.5.0 (#47745) --- recipes/snakemake-executor-plugin-slurm/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakemake-executor-plugin-slurm/meta.yaml b/recipes/snakemake-executor-plugin-slurm/meta.yaml index 06ad75219b25e3..51234b14bf3d12 100644 --- a/recipes/snakemake-executor-plugin-slurm/meta.yaml +++ b/recipes/snakemake-executor-plugin-slurm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "snakemake-executor-plugin-slurm" %} -{% set version = "0.4.5" %} +{% set version = "0.5.0" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/snakemake_executor_plugin_slurm-{{ version }}.tar.gz - sha256: 5b28371f17d81bb6287f35190fedd6cd50c78b62e21952cb30e4b4ba0b13d829 + sha256: 552b5dcf240829cc5ed3745d7e4f629c34b29ffcadfa48d3824219909537c216 build: noarch: python From aab6d1e508996eb7adbd9d3714112188fb7703e6 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 8 May 2024 03:35:04 +0300 Subject: [PATCH 08/81] jcvi: add linux-aarch64 build (#47155) * jcvi: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * ucsc-liftover: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Remove wrong addition unrelated to this PR Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/jcvi/meta.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/recipes/jcvi/meta.yaml b/recipes/jcvi/meta.yaml index fff106f59101fa..2d06ca554d10a8 100644 --- a/recipes/jcvi/meta.yaml +++ b/recipes/jcvi/meta.yaml @@ -11,7 +11,7 @@ source: build: skip: True # [py2k or osx] - number: 0 + number: 1 script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -80,3 +80,7 @@ about: license_file: LICENSE summary: Python utility libraries on genome assembly, annotation and comparative genomics description: "JCVI utility libraries" + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 7ca9ef5f4a7d9165d6fd6619a71983fa6740663a Mon Sep 17 00:00:00 2001 From: Clemens Schmid Date: Wed, 8 May 2024 03:17:04 +0200 Subject: [PATCH 09/81] Update poseidon-trident to 1.5.0.1 (#47741) * update poseidon-trident to v1.4.1.0 * update poseidon-trident --- recipes/poseidon-trident/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/poseidon-trident/meta.yaml b/recipes/poseidon-trident/meta.yaml index 16afdef2963008..fd463710cff8c4 100644 --- a/recipes/poseidon-trident/meta.yaml +++ b/recipes/poseidon-trident/meta.yaml @@ -1,13 +1,13 @@ -{% set version = "1.4.1.0" %} +{% set version = "1.5.0.1" %} package: name: poseidon-trident version: {{ version }} source: - url: https://github.com/poseidon-framework/poseidon-hs/releases/download/v{{ version }}/trident-conda-linux # [linux] - md5: 32399ef0bb0f0e0539b8e5de8da7909e # [linux] - - url: https://github.com/poseidon-framework/poseidon-hs/releases/download/v{{ version }}/trident-macOS # [osx] - md5: 8e84912883ee531c478a5e34158cfb05 # [osx] + md5: 71815ecd30b082610ca738130f04c933 # [linux] + - url: https://github.com/poseidon-framework/poseidon-hs/releases/download/v{{ version }}/trident-macOS-X64 # [osx] + md5: c7ce4930a046ee832b37558ed5799c8b # [osx] build: number: 0 From 10cec163f998b8dec51d48f324be39f17ee8f3f0 Mon Sep 17 00:00:00 2001 From: Clemens Schmid Date: Wed, 8 May 2024 03:17:12 +0200 Subject: [PATCH 10/81] Update poseidon-xerxes to 1.0.1.1 (#47743) --- recipes/poseidon-xerxes/meta.yaml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/recipes/poseidon-xerxes/meta.yaml b/recipes/poseidon-xerxes/meta.yaml index f5211ec3ba3fa4..efb89c986c0283 100644 --- a/recipes/poseidon-xerxes/meta.yaml +++ b/recipes/poseidon-xerxes/meta.yaml @@ -1,13 +1,13 @@ -{% set version = "1.0.0.2" %} +{% set version = "1.0.1.1" %} package: name: poseidon-xerxes version: {{ version }} source: - - url: https://github.com/poseidon-framework/poseidon-analysis-hs/releases/download/v{{ version }}/xerxes-Linux # [linux] - md5: 4fd78ba70641fa521425cb2b8f30be0b # [linux] - - url: https://github.com/poseidon-framework/poseidon-analysis-hs/releases/download/v{{ version }}/xerxes-macOS # [osx] - md5: 44899bc8bd82d9cb81903de9b3bbb914 # [osx] + - url: https://github.com/poseidon-framework/poseidon-analysis-hs/releases/download/v{{ version }}/xerxes-conda-linux # [linux] + md5: c1165839313a768ac12d1c8dbe7b2f0a # [linux] + - url: https://github.com/poseidon-framework/poseidon-analysis-hs/releases/download/v{{ version }}/xerxes-macOS-X64 # [osx] + md5: f101c7d0448b486b86edc259c7838a92 # [osx] build: number: 0 @@ -34,6 +34,6 @@ test: - xerxes --version about: - home: https://github.com/poseidon-framework/poseidon-analysis-hs + home: https://www.poseidon-adna.org/#/ license: MIT summary: "A tool (xerxes) to analyse genotype databases formatted using Poseidon." From b1406eda1797df529c3b2c74a70dea76e16e6814 Mon Sep 17 00:00:00 2001 From: Katherine Eaton Date: Tue, 7 May 2024 19:17:38 -0600 Subject: [PATCH 11/81] rebar: update from v0.2.0 to v0.2.1 (#47744) Co-authored-by: Katherine Eaton --- recipes/rebar/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/rebar/meta.yaml b/recipes/rebar/meta.yaml index 57c99e47b7c34b..1606b787686070 100644 --- a/recipes/rebar/meta.yaml +++ b/recipes/rebar/meta.yaml @@ -1,5 +1,5 @@ {% set name = "rebar" %} -{% set version = "0.2.0" %} +{% set version = "0.2.1" %} package: name: "{{ name|lower }}" @@ -7,9 +7,9 @@ package: source: - url: https://github.com/phac-nml/rebar/releases/download/v{{ version }}/{{ name }}-x86_64-unknown-linux-musl # [linux64] - sha256: 7b5648b353552662c66aab8347657dfebe92ee2d83e4a4f0b7a9526c58502b28 # [linux64] + sha256: f89184240277130a539e71994690eb3ec6ec4b2c45a851097dc261891e5a9f11 # [linux64] - url: https://github.com/phac-nml/rebar/releases/download/v{{ version }}/{{ name }}-x86_64-apple-darwin # [osx and x86_64] - sha256: b3577c5ea7965133fc5b934a9c4f9b5e1ba41603d5f9ce47fff79d6ee11adaa7 # [osx and x86_64] + sha256: 86b3df61488f3d9576c62ea13e13bac480d9531a142a3fc8f2ed72689ceff833 # [osx and x86_64] build: binary_relocation: False From 048518fde6e4c8c2e3308d2fb37c9aeebe585377 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gen=C3=ADs=20Bayarri?= Date: Wed, 8 May 2024 03:17:57 +0200 Subject: [PATCH 12/81] [biobb_io] update 4.1.1 (#47739) --- recipes/biobb_io/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/biobb_io/meta.yaml b/recipes/biobb_io/meta.yaml index 7754ec3c45deac..946fd09dfdb21c 100644 --- a/recipes/biobb_io/meta.yaml +++ b/recipes/biobb_io/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_io" %} -{% set version = "4.1.0" %} +{% set version = "4.1.1" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 074ea97a3682731e13d559b7f91b04e4a3f0f02ee798503089e4af79a730bf72 + sha256: 2bccb966ab28bc6f63d1f09309c1a300392643fbfaf66ca690f8f7fad7abe516 build: number: 0 @@ -45,7 +45,7 @@ about: \ building blocks that\ncreate new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest\ \ API documentation](http://biobb_io.readthedocs.io/en/latest/).\n\ \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\ - \n\n* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\ + \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\ Licensed under the\n\ [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\ \n\ From 68dc83b6205839598c4ff19879ae97409a054157 Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Tue, 7 May 2024 20:24:21 -0500 Subject: [PATCH 13/81] Update gmap to 2024-05-07 (#47750) --- recipes/gmap/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/gmap/meta.yaml b/recipes/gmap/meta.yaml index 4c3580f4d89710..83cf2311de6bda 100644 --- a/recipes/gmap/meta.yaml +++ b/recipes/gmap/meta.yaml @@ -1,6 +1,6 @@ {% set name = "GMAP" %} -{% set version = "2024.03.15" %} -{% set sha256 = "b3004175a06e3111d93021f0cd4d826ffa40ac4d069a2fa5db19fdaaa09fab3d" %} +{% set version = "2024.05.07" %} +{% set sha256 = "aa8ea153ec19977efa36983c5ec13ae77a92c9226a0a56ef5cc963b5e9edbd6e" %} package: name: {{ name|lower }} @@ -13,7 +13,7 @@ source: - single_quote_paths.patch build: - number: 2 + number: 0 run_exports: - {{ pin_subpackage('gmap', max_pin=None) }} @@ -43,6 +43,7 @@ about: license_family: APACHE license_file: LICENSE summary: "Genomic mapping and alignment program for mRNA and EST sequences." + dev_url: "http://research-pub.gene.com/gmap/" extra: additional-platforms: From 6bd366263151efa2757c578aff21537f8e82d1fc Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 8 May 2024 05:19:39 +0300 Subject: [PATCH 14/81] Add Linux aarch64 build for more Bioconductor packages (#47731) * Add Linux aarch64 build for more Bioconductor packages - chemminer - cnanorm - compass - cytolib - degseq - fgsea - linnorm - snprelate - snpstats Signed-off-by: Martin Tzvetanov Grigorov * Update cytolib to 2.14.1 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bioconductor-chemminer/meta.yaml | 4 +++- recipes/bioconductor-cnanorm/meta.yaml | 6 ++++-- recipes/bioconductor-compass/meta.yaml | 4 +++- recipes/bioconductor-cytolib/meta.yaml | 12 ++++++++---- recipes/bioconductor-degseq/meta.yaml | 6 ++++-- recipes/bioconductor-fgsea/meta.yaml | 4 +++- recipes/bioconductor-linnorm/meta.yaml | 7 ++++++- recipes/bioconductor-snprelate/meta.yaml | 8 ++++++-- recipes/bioconductor-snpstats/meta.yaml | 6 ++++-- 9 files changed, 41 insertions(+), 16 deletions(-) diff --git a/recipes/bioconductor-chemminer/meta.yaml b/recipes/bioconductor-chemminer/meta.yaml index dec3edb5902fc5..bd56196b89d1a2 100644 --- a/recipes/bioconductor-chemminer/meta.yaml +++ b/recipes/bioconductor-chemminer/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8dd1886811bdc4ac23c24fad60a9b238 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -70,6 +70,8 @@ about: summary: 'Cheminformatics Toolkit for R' description: 'ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:chemminer parent_recipe: diff --git a/recipes/bioconductor-cnanorm/meta.yaml b/recipes/bioconductor-cnanorm/meta.yaml index 0c80a7be466331..8a3abf24ba8c52 100644 --- a/recipes/bioconductor-cnanorm/meta.yaml +++ b/recipes/bioconductor-cnanorm/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b9d0f995f3466875285a152415863842 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -36,11 +36,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 + license: 'GPL-2-only' summary: 'A normalization method for Copy Number Aberration in cancer samples' description: 'Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:cnanorm parent_recipe: diff --git a/recipes/bioconductor-compass/meta.yaml b/recipes/bioconductor-compass/meta.yaml index 2948a0f2be468e..7b4d01bdbc6681 100644 --- a/recipes/bioconductor-compass/meta.yaml +++ b/recipes/bioconductor-compass/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6ab4a9ce40637244377f77b7baaecc38 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -75,6 +75,8 @@ about: summary: 'Combinatorial Polyfunctionality Analysis of Single Cells' description: 'COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject''s immune response to external stimuli such as infection or vaccination.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:compass - doi:10.1038/nbt.3187 diff --git a/recipes/bioconductor-cytolib/meta.yaml b/recipes/bioconductor-cytolib/meta.yaml index 9c473184d4d42d..d3c88990f43720 100644 --- a/recipes/bioconductor-cytolib/meta.yaml +++ b/recipes/bioconductor-cytolib/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.14.0" %} +{% set version = "2.14.1" %} {% set name = "cytolib" %} {% set bioc = "3.18" %} @@ -11,9 +11,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - md5: f06a976c84ae2adf3c08d07cd90af7f4 + md5: 32b6560c381660e2ed9aa1e7b6ab84f9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -43,11 +43,15 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: AGPL-3.0-only + license: GPL-3.0-only summary: 'C++ infrastructure for representing and interacting with the gated cytometry data' description: 'This package provides the core data structure and API to represent and interact with the gated cytometry data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} parent_recipe: name: bioconductor-cytolib path: recipes/bioconductor-cytolib diff --git a/recipes/bioconductor-degseq/meta.yaml b/recipes/bioconductor-degseq/meta.yaml index 1fd5c9056f4009..6d4d4a1ad423bc 100644 --- a/recipes/bioconductor-degseq/meta.yaml +++ b/recipes/bioconductor-degseq/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cc89e25cb7e9afc38b5fb2bba34722b5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -36,11 +36,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>=2)' + license: 'LGPL-3-or-above' summary: 'Identify Differentially Expressed Genes from RNA-seq data' description: 'DEGseq is an R package to identify differentially expressed genes from RNA-Seq data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:degseq - doi:10.1093/bioinformatics/btp612 diff --git a/recipes/bioconductor-fgsea/meta.yaml b/recipes/bioconductor-fgsea/meta.yaml index 1d179f86b50b26..8463d4f6d6021e 100644 --- a/recipes/bioconductor-fgsea/meta.yaml +++ b/recipes/bioconductor-fgsea/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 53b8ab8a13390a0920bc13eeba3aa1b8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -58,6 +58,8 @@ about: summary: 'Fast Gene Set Enrichment Analysis' description: 'The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:fgsea - doi:10.1101/060012 diff --git a/recipes/bioconductor-linnorm/meta.yaml b/recipes/bioconductor-linnorm/meta.yaml index 5c346153764e99..baa5b5fdfc69a3 100644 --- a/recipes/bioconductor-linnorm/meta.yaml +++ b/recipes/bioconductor-linnorm/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8fc0ff0d6e9c2d274137b0e99ce0f4a2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -76,3 +76,8 @@ about: description: 'Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large scale count data. It has been independently reviewed by Tian et al. on Nature Methods (https://doi.org/10.1038/s41592-019-0425-8). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM.' license_file: LICENSE +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-snprelate/meta.yaml b/recipes/bioconductor-snprelate/meta.yaml index a0e37b7d6801ad..2fac4055b5d28b 100644 --- a/recipes/bioconductor-snprelate/meta.yaml +++ b/recipes/bioconductor-snprelate/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: f4e5095c6b99014e02d770e7f4bd5617 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -37,11 +37,15 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3-only summary: 'Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data' description: 'Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls in whole-genome and whole-exome variant data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} parent_recipe: name: bioconductor-snprelate path: recipes/bioconductor-snprelate diff --git a/recipes/bioconductor-snpstats/meta.yaml b/recipes/bioconductor-snpstats/meta.yaml index 0203a1cda44813..8843ee6bc567ee 100644 --- a/recipes/bioconductor-snpstats/meta.yaml +++ b/recipes/bioconductor-snpstats/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0625c920470937a31fd278cf8bd8982a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -42,11 +42,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: 'GPL-3-only' summary: 'SnpMatrix and XSnpMatrix classes and methods' description: 'Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:snpstats - doi:10.1038/nmeth.3252 From f0908ab4d0b18261c9dd1f6924808e923d60f75d Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Wed, 8 May 2024 05:20:33 +0300 Subject: [PATCH 15/81] Add Linux aarch64 build for more Bioconductor packages (#47730) * Add Linux aarch64 build for more Bioconductor packages - affyio - beclear - bus - ebimage - edger - graph - rhdf5filters - sparsematrixstats Signed-off-by: Martin Tzvetanov Grigorov * Do not build ebimage for now - it fails on OSX Update edgeR to 4.0.16 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bioconductor-affyio/meta.yaml | 6 ++++-- recipes/bioconductor-beclear/meta.yaml | 6 ++++-- recipes/bioconductor-bus/meta.yaml | 6 ++++-- recipes/bioconductor-edger/meta.yaml | 10 ++++++---- recipes/bioconductor-graph/meta.yaml | 4 +++- recipes/bioconductor-rhdf5filters/meta.yaml | 7 ++++++- recipes/bioconductor-sparsematrixstats/meta.yaml | 7 ++++++- 7 files changed, 33 insertions(+), 13 deletions(-) diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml index 0338d5377855c4..7e1bef9f6ac341 100644 --- a/recipes/bioconductor-affyio/meta.yaml +++ b/recipes/bioconductor-affyio/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 9bd1e4acedbf756386f96d4c1ebb21f3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -36,11 +36,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2)' + license: 'LGPL-3.0-or-later' summary: 'Tools for parsing Affymetrix data files' description: 'Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:affyio - doi:10.1038/nmeth.3252 diff --git a/recipes/bioconductor-beclear/meta.yaml b/recipes/bioconductor-beclear/meta.yaml index 22a3733efe5e52..5c7b037c6d71c5 100644 --- a/recipes/bioconductor-beclear/meta.yaml +++ b/recipes/bioconductor-beclear/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: bd34703e5a35dfc888f0029395df2c80 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -54,11 +54,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: 'GPL-3.0-only' summary: 'Correction of batch effects in DNA methylation data' description: 'Provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:beclear - doi:10.1371/journal.pone.0159921 diff --git a/recipes/bioconductor-bus/meta.yaml b/recipes/bioconductor-bus/meta.yaml index d0b152aca8a537..ba7572a4353024 100644 --- a/recipes/bioconductor-bus/meta.yaml +++ b/recipes/bioconductor-bus/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 788ab26ecf05f0df93667a7c37f564ff build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -38,11 +38,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: 'GPL-3.0-only' summary: 'Gene network reconstruction' description: 'This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:bus - doi:10.1038/nmeth.3252 diff --git a/recipes/bioconductor-edger/meta.yaml b/recipes/bioconductor-edger/meta.yaml index 0884137cf6b49e..b8f25cddfaf0d9 100644 --- a/recipes/bioconductor-edger/meta.yaml +++ b/recipes/bioconductor-edger/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "4.0.2" %} +{% set version = "4.0.16" %} {% set name = "edgeR" %} {% set bioc = "3.18" %} @@ -11,9 +11,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 0ba48556be0c95b929db5bbed32923f3 + md5: 8fb1c6c67e29d299c991d16d0f6c5f5b build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -41,11 +41,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' + license: 'GPL-3.0-or-later' summary: 'Empirical Analysis of Digital Gene Expression Data in R' description: 'Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:edger - usegalaxy-eu:edger diff --git a/recipes/bioconductor-graph/meta.yaml b/recipes/bioconductor-graph/meta.yaml index 79a97be096508f..3d9995b0183a98 100644 --- a/recipes/bioconductor-graph/meta.yaml +++ b/recipes/bioconductor-graph/meta.yaml @@ -15,7 +15,7 @@ source: patches: - patch build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -42,6 +42,8 @@ about: summary: 'graph: A package to handle graph data structures' description: 'A package that implements some simple graph handling capabilities.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:graph - doi:10.1038/nmeth.3252 diff --git a/recipes/bioconductor-rhdf5filters/meta.yaml b/recipes/bioconductor-rhdf5filters/meta.yaml index 8d776ef5256622..b28d9aa1fb49bb 100644 --- a/recipes/bioconductor-rhdf5filters/meta.yaml +++ b/recipes/bioconductor-rhdf5filters/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3ecb2d30759fee6bde37bbb1f90fbf79 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -43,4 +43,9 @@ about: summary: 'HDF5 Compression Filters' description: 'Provides a collection of additional compression filters for HDF5 datasets. The package is intended to provide seemless integration with rhdf5, however the compiled filters can also be used with external applications.' license_file: LICENSE +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name }} diff --git a/recipes/bioconductor-sparsematrixstats/meta.yaml b/recipes/bioconductor-sparsematrixstats/meta.yaml index 5b0186e8e00f31..b32bbcc2f9c2f7 100644 --- a/recipes/bioconductor-sparsematrixstats/meta.yaml +++ b/recipes/bioconductor-sparsematrixstats/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4319e6fb04b91467bd08cc4ce2ad609c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -48,4 +48,9 @@ about: summary: 'Summary Statistics for Rows and Columns of Sparse Matrices' description: 'High performance functions for row and column operations on sparse matrices. For example: col / rowMeans2, col / rowMedians, col / rowVars etc. Currently, the optimizations are limited to data in the column sparse format. This package is inspired by the matrixStats package by Henrik Bengtsson.' license_file: LICENSE +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name }} From 7f26b04c5eb4c5edc1695b658554a579bbae454b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Florian=20Plaza=20O=C3=B1ate?= <4588656+fplazaonate@users.noreply.github.com> Date: Wed, 8 May 2024 04:22:00 +0200 Subject: [PATCH 16/81] New version and better tests (#47705) --- recipes/crocodeel/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/crocodeel/meta.yaml b/recipes/crocodeel/meta.yaml index ecbd75bb5842c8..e6f885fdba0704 100644 --- a/recipes/crocodeel/meta.yaml +++ b/recipes/crocodeel/meta.yaml @@ -1,5 +1,5 @@ {% set name = "crocodeel" %} -{% set version = "1.0.2" %} +{% set version = "1.0.3" %} package: name: {{ name }} @@ -8,7 +8,7 @@ package: source: url: https://github.com/metagenopolis/{{ name }}/archive/v{{ version }}.tar.gz - sha256: 4ac427b0f1ad2e58b1e7256895442fe632fc9941194f9059ce59af2d0007a15c + sha256: f9d7de8fe83ea3b645cc8f11c45d1ddf1d79fd163870f013282a11a862b45f77 build: noarch: python @@ -33,7 +33,7 @@ requirements: test: commands: - - crocodeel -h + - crocodeel test_install about: home: https://github.com/metagenopolis/crocodeel From 61f449b73d00295b8cc096477049151bc8523d83 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Tue, 7 May 2024 23:39:06 -0400 Subject: [PATCH 17/81] Update stringtie to 2.2.3 (#47751) * Update stringtie to 2.2.3 * test osx build * edit meta.yaml * edit meta.yaml * edit meta.yaml --------- Co-authored-by: mencian --- recipes/stringtie/build.sh | 5 +- recipes/stringtie/build_failure.linux-64.yaml | 104 ------------------ recipes/stringtie/meta.yaml | 21 ++-- 3 files changed, 14 insertions(+), 116 deletions(-) delete mode 100644 recipes/stringtie/build_failure.linux-64.yaml diff --git a/recipes/stringtie/build.sh b/recipes/stringtie/build.sh index cb22d7d1094078..36aa92faf72741 100644 --- a/recipes/stringtie/build.sh +++ b/recipes/stringtie/build.sh @@ -1,6 +1,6 @@ -#!/bin/sh +#!/bin/bash -ln -s $PREFIX/lib/libz.so.1 $PREFIX/lib/libz.so +ln -sf $PREFIX/lib/libz.so.1 $PREFIX/lib/libz.so export C_INCLUDE_PATH=$PREFIX/include export CPLUS_INCLUDE_PATH=$PREFIX/include @@ -9,6 +9,7 @@ export CXXFLAGS="$CPPFLAGS" make release CXX=$CXX mkdir -p $PREFIX/bin +chmod 755 stringtie mv stringtie $PREFIX/bin # Prepare prepDE diff --git a/recipes/stringtie/build_failure.linux-64.yaml b/recipes/stringtie/build_failure.linux-64.yaml deleted file mode 100644 index 13ad838251ba55..00000000000000 --- a/recipes/stringtie/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 3dbc68fc7b66d4c21c2045d31273d3244a913d7ed183dc762baa1f87cbd1c61b # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - rlink.cpp:11677:41: note: '*(void**)((char*)&trpattern offsetof(GBitVec, GBitVec::fBits))' was declared here - 11677 | GBitVec trpattern(transfrag[t]->pattern); - | ^~~~~~~~~ - In function 'bool GMalloc(void**, long unsigned int)', - inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:158:5, - inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:150:3, - inlined from 'GBitVec traverse_dfs(int, int, CGraphnode*, CGraphnode*, GBitVec, int, GVec&, GPVec**, GPVec**, int&, GIntHash**, int&)' at rlink.cpp:2484:53: - ./gclib/GBase.h:254:12: warning: '*(void**)((char*)& offsetof(GBitVec, GBitVec::fBits))' may be used uninitialized [-Wmaybe-uninitialized] - 254 | return *ptr!=NULL; - | ^~~~ - rlink.cpp: In function 'GBitVec traverse_dfs(int, int, CGraphnode*, CGraphnode*, GBitVec, int, GVec&, GPVec**, GPVec**, int&, GIntHash**, int&)': - rlink.cpp:2484:63: note: '' declared here - 2484 | node->childpat = node->childpat | traverse_dfs(s,g,no2gnode[s][g][node->child[i]],sink,childparents,gno,visit,no2gnode,transfrag,edgeno,gpos,lastgpos); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:159:11, - inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:150:3, - inlined from 'GBitVec traverse_dfs(int, int, CGraphnode*, CGraphnode*, GBitVec, int, GVec&, GPVec**, GPVec**, int&, GIntHash**, int&)' at rlink.cpp:2461:28: - /opt/conda/conda-bld/stringtie_1685392826475/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/bits/string3.h:52:33: warning: '*(void**)((char*)&childparents offsetof(GBitVec, GBitVec::fBits))' may be used uninitialized [-Wmaybe-uninitialized] - 52 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - rlink.cpp: In function 'GBitVec traverse_dfs(int, int, CGraphnode*, CGraphnode*, GBitVec, int, GVec&, GPVec**, GPVec**, int&, GIntHash**, int&)': - rlink.cpp:2461:25: note: '*(void**)((char*)&childparents offsetof(GBitVec, GBitVec::fBits))' was declared here - 2461 | GBitVec childparents=parents; - | ^~~~~~~~~~~~ - In function 'bool GMalloc(void**, long unsigned int)', - inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:158:5, - inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:150:3, - inlined from 'int create_graph(int, int, int, CBundle*, GPVec&, GList&, GList&, GVec**, GPVec**, GPVec**, GIntHash**, BundleData*, int&, int&, GArray&, int)' at rlink.cpp:3623:14: - ./gclib/GBase.h:254:12: warning: '*(void**)((char*)& offsetof(GBitVec, GBitVec::fBits))' may be used uninitialized [-Wmaybe-uninitialized] - 254 | return *ptr!=NULL; - | ^~~~ - rlink.cpp: In function 'int create_graph(int, int, int, CBundle*, GPVec&, GList&, GList&, GVec**, GPVec**, GPVec**, GIntHash**, BundleData*, int&, int&, GArray&, int)': - rlink.cpp:3623:21: note: '' declared here - 3623 | traverse_dfs(s,g,source,sink,parents,graphno,visit,no2gnode,transfrag,edgeno,gpos,lastgpos); - | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - In function 'void* memcpy(void*, const void*, size_t)', - inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:159:11, - inlined from 'GBitVec::GBitVec(const GBitVec&)' at ./gclib/GBitVec.h:150:3, - inlined from 'void get_fragment_pattern(GList&, int, int, float, GVec*, GVec&, GVec*, GVec**, GVec*, GVec*, GIntHash**, GPVec**, GPVec**, CTreePat***, GPVec&)' at rlink.cpp:4350:34: - /opt/conda/conda-bld/stringtie_1685392826475/_build_env/x86_64-conda-linux-gnu/sysroot/usr/include/bits/string3.h:52:33: warning: '*(void**)((char*)&conflictpattn offsetof(GBitVec, GBitVec::fBits))' may be used uninitialized [-Wmaybe-uninitialized] - 52 | return __builtin___memcpy_chk (__dest, __src, __len, __bos0 (__dest)); - | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - rlink.cpp: In function 'void get_fragment_pattern(GList&, int, int, float, GVec*, GVec&, GVec*, GVec**, GVec*, GVec*, GIntHash**, GPVec**, GPVec**, CTreePat***, GPVec&)': - rlink.cpp:4350:41: note: '*(void**)((char*)&conflictpattn offsetof(GBitVec, GBitVec::fBits))' was declared here - 4350 | GBitVec conflictpattn=gnode->parentpat; - | ^~~~~~~~~~~~~ - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DNDEBUG -Wall -Wextra -I. -I./gclib -I$PREFIX/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tablemaker.cpp -o tablemaker.o - tablemaker.cpp: In function 'void rc_update_exons(RC_BundleData&)': - tablemaker.cpp:205:29: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 205 | bind2nd( minus(), avg)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ - In file included from /opt/conda/conda-bld/stringtie_1685392826475/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/bits/stl_function.h:1438, - from /opt/conda/conda-bld/stringtie_1685392826475/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/functional:49, - from ./gclib/khashl.hh:25, - from ./gclib/GHashMap.hh:8, - from ./gclib/GFastaIndex.h:11, - from ./gclib/GFaSeqGet.h:3, - from ./gclib/gff.h:9, - from rlink.h:5, - from tablemaker.cpp:2: - /opt/conda/conda-bld/stringtie_1685392826475/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ - tablemaker.cpp:212:29: warning: 'std::binder2nd<_Operation> std::bind2nd(const _Operation&, const _Tp&) [with _Operation = minus; _Tp = double]' is deprecated: use 'std::bind' instead [-Wdeprecated-declarations] - 212 | bind2nd( minus(), mavg)); - | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ - /opt/conda/conda-bld/stringtie_1685392826475/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/backward/binders.h:172:5: note: declared here - 172 | bind2nd(const _Operation& __fn, const _Tp& __x) - | ^~~~~~~ - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DNDEBUG -Wall -Wextra -I. -I./gclib -I$PREFIX/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c tmerge.cpp -o tmerge.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DNDEBUG -Wall -Wextra -I. -I./gclib -I$PREFIX/include/htslib -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -std=c11 -fno-strict-aliasing -fno-exceptions -fno-rtti -Wno-implicit-fallthrough -Wno-class-memaccess -pthread -c stringtie.cpp -o stringtie.o - stringtie.cpp: In function 'int main(int, char**)': - stringtie.cpp:468:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] - 468 | if (tstackSize - sys.exit(main()) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/stringtie_1685392826475/work/conda_build.sh']' returned non-zero exit status 35. -# Last 100 lines of the build log. diff --git a/recipes/stringtie/meta.yaml b/recipes/stringtie/meta.yaml index fe28cb6bc9bc50..37148fc6c28044 100644 --- a/recipes/stringtie/meta.yaml +++ b/recipes/stringtie/meta.yaml @@ -1,6 +1,6 @@ {% set name = "StringTie" %} -{% set version = "2.2.2" %} -{% set sha256 = "f75f23b8466898d27984fb99cf6f828094fb3ed0307aed7af76e334acb997010" %} +{% set version = "2.2.3" %} +{% set sha256 = "f372640b70a8fde763712d2f0565aff71f5facdc2300c8af829fea94a05ff208" %} package: name: {{ name|lower }} @@ -14,18 +14,18 @@ source: build: number: 0 - run_exports: - - {{ pin_subpackage("stringtie", max_pin="x.x") }} # TODO currently fails to build on osx. # Feel free to re-enable and debug. - skip: true # [osx] + skip: True # [osx] + run_exports: + - {{ pin_subpackage("stringtie", max_pin="x") }} requirements: build: - make - - zlib - {{ compiler('c') }} - {{ compiler('cxx') }} + - zlib host: # curl is used to download prepDE.py - htslib @@ -39,18 +39,19 @@ test: - prepDE.py --help about: - home: https://ccb.jhu.edu/software/stringtie/ + home: "https://ccb.jhu.edu/software/stringtie" license: MIT license_file: LICENSE license_family: MIT - summary: "StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts." - dev_url: https://github.com/gpertea/stringtie + summary: "StringTie employs efficient algorithms for transcript structure recovery and abundance estimation from bulk RNA-Seq reads aligned to a reference genome." + dev_url: "https://github.com/gpertea/stringtie" + doc_url: "https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual" extra: additional-platforms: - linux-aarch64 identifiers: - - biotools:StringTie + - biotools:stringtie - usegalaxy-eu:stringtie - doi:10.1038/nbt.3122 - doi:10.1038/nprot.2016.095 From 362207eed78a1f35850c0c6ea689818a97588dc9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 00:43:52 -0400 Subject: [PATCH 18/81] Update jcvi to 1.4.9 (#47752) * Update jcvi to 1.4.9 * test osx build * edit meta.yaml * edit meta.yaml * edit meta.yaml --------- Co-authored-by: mencian --- recipes/jcvi/meta.yaml | 37 +++++++++++++++++++------------------ 1 file changed, 19 insertions(+), 18 deletions(-) diff --git a/recipes/jcvi/meta.yaml b/recipes/jcvi/meta.yaml index 2d06ca554d10a8..f18b58e7601325 100644 --- a/recipes/jcvi/meta.yaml +++ b/recipes/jcvi/meta.yaml @@ -1,18 +1,20 @@ {% set name = "jcvi" %} -{% set version = "1.3.9" %} +{% set version = "1.4.9" %} package: - name: '{{ name|lower }}' - version: '{{ version }}' + name: {{ name }} + version: {{ version }} source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 495940ed40e419a32c8b9dc9582fe64e233edf8d796fca71422223c3494ceaa8 + sha256: 0cb2f8339169456b4fadf3767af59d5eac36ff74e8eb30885ebbbc944c83079d build: - skip: True # [py2k or osx] - number: 1 - script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv + skip: True # [osx] + number: 0 + script_env: + - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }} + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv run_exports: - {{ pin_subpackage(name, max_pin='x') }} @@ -22,8 +24,9 @@ requirements: host: - python - pip - - numpy + - setuptools-scm - cython + - numpy run: - python - biopython @@ -39,20 +42,16 @@ requirements: - matplotlib-base - natsort - networkx - - numpy + - {{ pin_compatible('numpy') }} - pypdf2 - more-itertools - - r-ggplot2 - last + - r-ggplot2 - r-tinytex - #- pytest - #- pytest-benchmark - #- pytest-cov - pyyaml - rich - scipy - seaborn-base - #- texlive-core - ucsc-liftover test: @@ -71,16 +70,18 @@ test: - jcvi.variation #This fails for some unknown reason, even though it's outputting "JCVI utility libraries" #commands: - # - "python -m jcvi.apps 2>&1 | grep 'JCVI utility libraries'" + # - 'python -m jcvi.apps 2>&1 | grep "JCVI utility libraries"' about: - home: http://github.com/tanghaibao/jcvi + home: "https://github.com/tanghaibao/jcvi" license: BSD-2-Clause license_family: BSD license_file: LICENSE - summary: Python utility libraries on genome assembly, annotation and comparative genomics + summary: "Python utility libraries on genome assembly, annotation, and comparative genomics" description: "JCVI utility libraries" + dev_url: "https://github.com/tanghaibao/jcvi" + doc_url: "https://github.com/tanghaibao/jcvi/wiki" extra: additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 From 61972b1b3a66027acb194707c1adb4512f18efed Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 00:44:01 -0400 Subject: [PATCH 19/81] Update oakvar to 2.9.123 (#47754) --- recipes/oakvar/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/oakvar/meta.yaml b/recipes/oakvar/meta.yaml index 91c6fe040ca8bd..379d8b05e88098 100644 --- a/recipes/oakvar/meta.yaml +++ b/recipes/oakvar/meta.yaml @@ -1,6 +1,6 @@ {% set name = "OakVar" %} -{% set version = "2.9.122" %} -{% set sha256 = "cd806f2c6c98ab2de147fe6ae59d2826e36d3ac58b961b2c34c38ee2912cd8ad" %} +{% set version = "2.9.123" %} +{% set sha256 = "6094cc2a65ce780bd6b05ad9919b107eaefc4ea329daf7856a6a09d48e48bbf1" %} package: name: {{ name|lower }} From 77e3b4a189c9cd310ef51028df7cfa85adc63265 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 02:06:27 -0400 Subject: [PATCH 20/81] Update snakefmt to 0.10.2 (#47755) --- recipes/snakefmt/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/snakefmt/meta.yaml b/recipes/snakefmt/meta.yaml index 91ea56d632d399..993a11f02aaa8d 100644 --- a/recipes/snakefmt/meta.yaml +++ b/recipes/snakefmt/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.10.1" %} +{% set version = "0.10.2" %} package: name: snakefmt @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/s/snakefmt/snakefmt-{{ version }}.tar.gz - sha256: b04a34fc5481b15667c8bc7f23b5722b98ef827b27c6fd6dfbab8b34b245e32b + sha256: 4286a5903b66da7e52763c5e8184da4edc95113b758f4448528804fb54f9b75a build: number: 0 From 2130d962905eea1de9074df74f71d5dd3c188d62 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 04:39:59 -0400 Subject: [PATCH 21/81] Update bioconda-utils to 2.15.1 (#47759) * Update bioconda-utils to 2.15.1 * bioconda-utils: Add dep conda-package-streaming --------- Co-authored-by: Marcel Bargull --- recipes/bioconda-utils/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 8268fc56873f49..d81622d3d80432 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,6 +1,6 @@ {% set name = "bioconda-utils" %} -{% set version = "2.15.0" %} -{% set sha256 = "d4d0985220481fb2654e0f5743a2784befac1d59a52cc275ebebce52cee01fa4" %} +{% set version = "2.15.1" %} +{% set sha256 = "729f00c8ca5b3c7f469215edfc8122aa8617111b3151ed359081cc6a4b4f1a24" %} package: name: {{ name }} @@ -12,7 +12,7 @@ source: build: noarch: python - number: 1 + number: 0 script: {{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv entry_points: - bioconda-utils = bioconda_utils.cli:main @@ -30,6 +30,7 @@ requirements: - conda-libmamba-solver 24.1.* - conda-build 24.3.* - conda-index 0.4.* + - conda-package-streaming 0.9.* - mamba 1.5.* - boa 0.17.* - argh 0.31.* From 4d44d3ed910d1ec5682510b113a210190a17ff06 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gen=C3=ADs=20Bayarri?= Date: Wed, 8 May 2024 10:43:30 +0200 Subject: [PATCH 22/81] [biobb_vs] update 4.1.2 (#47762) --- recipes/biobb_vs/meta.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/biobb_vs/meta.yaml b/recipes/biobb_vs/meta.yaml index 8f640424a3df3e..fa719eccc4297b 100644 --- a/recipes/biobb_vs/meta.yaml +++ b/recipes/biobb_vs/meta.yaml @@ -1,5 +1,5 @@ {% set name = "biobb_vs" %} -{% set version = "4.1.1" %} +{% set version = "4.1.2" %} package: name: '{{ name|lower }}' @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0be7e032922617797552024ee942cb3f99ecfb125cb767ba0f80a38f43402224 + sha256: a0f8f09859ae547c7fbc33f637de6eb41546f175abe6274570c90467839b8dd5 build: number: 0 @@ -22,12 +22,12 @@ requirements: - setuptools - biobb_common ==4.1.0 - vina ==1.2.3 - - fpocket >=3.1.4.2 + - fpocket ==4.1 run: - python >=3.8 - biobb_common ==4.1.0 - vina ==1.2.3 - - fpocket >=3.1.4.2 + - fpocket ==4.1 test: imports: @@ -45,7 +45,7 @@ about: description: "# biobb_vs\n\n### Introduction\nBiobb_vs is the Biobb module collection to perform virtual screening studies.\nBiobb (BioExcel building blocks) packages are Python building blocks that\ncreate\ \ new layer of compatibility and interoperability over popular\nbioinformatics tools.\nThe latest documentation of this package can be found in our readthedocs site:\n[latest API documentation](http://biobb-vs.readthedocs.io/en/latest/).\n\ \n\n### Copyright & Licensing\nThis software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).\ - \n\n* (c) 2015-2023 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2023 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\ + \n\n* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)\n* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)\n\ Licensed under the\n\ [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.\n\ \n\ From 62be6c384382e232692fa666e782550154cb9e40 Mon Sep 17 00:00:00 2001 From: Marcel Bargull Date: Wed, 8 May 2024 13:41:01 +0200 Subject: [PATCH 23/81] CI: use correct build-env container for aarch64 (#47767) Signed-off-by: Marcel Bargull --- .circleci/config.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 7020f97145379a..201b46c7dea432 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -53,12 +53,13 @@ jobs: # a basic unit of work in a run - run: name: Build and test command: | + . common.sh source /opt/mambaforge/etc/profile.d/conda.sh source /opt/mambaforge/etc/profile.d/mamba.sh mamba activate bioconda bioconda-utils build recipes config.yml \ --lint --docker --mulled-test \ - --docker-base-image quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch) \ + --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \ --git-range origin/master HEAD - run: @@ -201,6 +202,7 @@ jobs: # a basic unit of work in a run name: Build and upload command: | set -e + . common.sh source /opt/mambaforge/etc/profile.d/conda.sh source /opt/mambaforge/etc/profile.d/mamba.sh mamba activate bioconda @@ -211,7 +213,7 @@ jobs: # a basic unit of work in a run echo '============' bioconda-utils build recipes config.yml \ --worker-offset << parameters.runner >> --n-workers 6 \ - --docker --mulled-test --docker-base-image quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch) \ + --docker --mulled-test --docker-base-image "quay.io/bioconda/bioconda-utils-build-env-cos7-$(arch):${BIOCONDA_UTILS_TAG#v}" \ --anaconda-upload \ --mulled-upload-target biocontainers \ --record-build-failures \ From c3446a10912cfc214467cf1a3d341a7677b7eaf9 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 08:07:33 -0400 Subject: [PATCH 24/81] Update annonars to 0.36.2 (#47766) * Update annonars to 0.36.2 * Update meta.yaml --------- Co-authored-by: Manuel Holtgrewe --- recipes/annonars/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/annonars/meta.yaml b/recipes/annonars/meta.yaml index c07360cdd3eb2f..fa23534ad1dd21 100644 --- a/recipes/annonars/meta.yaml +++ b/recipes/annonars/meta.yaml @@ -1,18 +1,18 @@ -{% set version = "0.36.1" %} +{% set version = "0.36.2" %} package: name: annonars version: {{ version }} build: - number: 1 + number: 0 skip: True # [osx] run_exports: - {{ pin_subpackage("annonars", max_pin="x.x") }} source: url: https://github.com/varfish-org/annonars/archive/refs/tags/v{{ version }}.tar.gz - sha256: 7aee8b87780956171a922b8fead5201c1506d5ec9cadc7ea33c009ce2f0b3816 + sha256: 89b39a7e08ceb33ffc99364396222fffdda7e2fabd313bebf2976b365ed057c3 requirements: build: @@ -45,5 +45,6 @@ about: extra: recipe-maintainers: - holtgrewe + - tedil additional-platforms: - linux-aarch64 From 506e0a2db32fa7116a50a6230af4e5fcb28d6c71 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 10:44:15 -0400 Subject: [PATCH 25/81] Update argnorm to 0.3.0 (#47761) --- recipes/argnorm/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/argnorm/meta.yaml b/recipes/argnorm/meta.yaml index 3266c5db324335..0b5d31ed0e52b9 100644 --- a/recipes/argnorm/meta.yaml +++ b/recipes/argnorm/meta.yaml @@ -1,5 +1,5 @@ {% set name = "argnorm" %} -{% set version = "0.2.0" %} +{% set version = "0.3.0" %} package: name: "{{ name|lower }}" @@ -7,11 +7,11 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 8210aaa121272f2bd815498332bd076b9a5322b064c851dfb32d01486921a88c + sha256: 32ae41d1c099558b3257f88dd5ff34e70614646dec5bbf6fd7e0b30f816a5f57 build: noarch: python - number: 1 + number: 0 entry_points: - argnorm=argnorm.cli:main script: "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" From 4d857811827ce10ad06610c2029111941700e9e2 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 10:44:24 -0400 Subject: [PATCH 26/81] Update cgelib to 0.7.5 (#47765) --- recipes/cgelib/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/cgelib/meta.yaml b/recipes/cgelib/meta.yaml index ddbcd260e9cc19..e36cc291d16298 100644 --- a/recipes/cgelib/meta.yaml +++ b/recipes/cgelib/meta.yaml @@ -1,5 +1,5 @@ {% set name = "cgelib" %} -{% set version = "0.7.4" %} +{% set version = "0.7.5" %} package: name: {{ name|lower }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/cgelib-{{ version }}.tar.gz - sha256: 213181bba24856ec367bdfd1e4615eeefff88243f8d29ad9446150927a434aed + sha256: f125106027dd4998dca8b73e2a558fc2fa2bbc968632162203fb3d93beb04452 build: number: 0 From bd6da427e5e14c06ce1ddef4e7db5924b77324a6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 12:07:01 -0400 Subject: [PATCH 27/81] Update sequali to 0.8.0 (#47769) --- recipes/sequali/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sequali/meta.yaml b/recipes/sequali/meta.yaml index 6efff8664aeb62..efb09494250a33 100644 --- a/recipes/sequali/meta.yaml +++ b/recipes/sequali/meta.yaml @@ -1,5 +1,5 @@ {% set name = "sequali" %} -{% set version = "0.7.1" %} +{% set version = "0.8.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 4c77a54e986c8afbac80e3cc5511b0b1a53e6d8572db11ea691edd83fa58e08c + sha256: 88253eba36be929b37dc8dbf9c81ff14a8d76491943fa035f74e7a4faac90272 build: number: 0 From f40be7dc89e87fe14b481a97bc2d8a47df025e64 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 12:33:35 -0400 Subject: [PATCH 28/81] Update jcvi to 1.4.10 (#47768) --- recipes/jcvi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jcvi/meta.yaml b/recipes/jcvi/meta.yaml index f18b58e7601325..74e4055bb11ca7 100644 --- a/recipes/jcvi/meta.yaml +++ b/recipes/jcvi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "jcvi" %} -{% set version = "1.4.9" %} +{% set version = "1.4.10" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 0cb2f8339169456b4fadf3767af59d5eac36ff74e8eb30885ebbbc944c83079d + sha256: 3c9763e6dbe3a85bc9f66f835814edaaf2929142179dc03f5a79536358117026 build: skip: True # [osx] From 54356135bbfe9bfeaf91211e0ec5f6e533f3929c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 19:49:42 -0400 Subject: [PATCH 29/81] Update gtotree to 1.8.6 (#47781) --- recipes/gtotree/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gtotree/meta.yaml b/recipes/gtotree/meta.yaml index 5924741cf9630b..6955b5089cf726 100644 --- a/recipes/gtotree/meta.yaml +++ b/recipes/gtotree/meta.yaml @@ -1,5 +1,5 @@ {% set name = "GToTree" %} -{% set version = "1.8.5" %} +{% set version = "1.8.6" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: https://github.com/AstrobioMike/GToTree/archive/v{{ version }}.tar.gz - sha256: a74e2a824cb79cfb50ed8bfcad11d4db98d7f485da38d9c3af83a0bebcb0cdca + sha256: 1712d9e18f128bbeeb585b1528a8e207c3a36cc7f1dbb7df66416ec0278d5a9a build: number: 0 From 1d1ce528c9413242f7ff379107cab60b07ab98b5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 21:33:23 -0400 Subject: [PATCH 30/81] Update instrain to 1.9.0 (#47770) --- recipes/instrain/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/instrain/meta.yaml b/recipes/instrain/meta.yaml index b3390694f61730..04043ba16bc95f 100644 --- a/recipes/instrain/meta.yaml +++ b/recipes/instrain/meta.yaml @@ -1,5 +1,5 @@ {% set name = "inStrain" %} -{% set version = "1.8.1" %} +{% set version = "1.9.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: 0eab49f8f4bd64037f4314c228a193f6dfeaf37dec96eee81cf63851adeb9a59 + sha256: 723c24c3eaff262c703213beedf2da36b9a198ae8ad9f0168a379348c386d7d2 build: noarch: python From 5f23d710ef63c487f03c56095212f9410bb5cd7e Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 21:33:33 -0400 Subject: [PATCH 31/81] Update wgd to 2.0.37 (#47771) * Update wgd to 2.0.36 * Update wgd to 2.0.37 --- recipes/wgd/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/wgd/meta.yaml b/recipes/wgd/meta.yaml index b7523c87b344c0..f5b1b6352f0205 100644 --- a/recipes/wgd/meta.yaml +++ b/recipes/wgd/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.35" %} +{% set version = "2.0.37" %} package: name: "wgd" @@ -6,7 +6,7 @@ package: source: url: https://pypi.io/packages/source/w/wgd/wgd-{{ version }}.tar.gz - sha256: d1feaaebf2d2645652b8aee0d9113d19ed48dfd429dcd818320a2452ccab2a52 + sha256: 9a9a1f7dda9da1907ed108ed5c74a7cc739492405488fe1e9a538595d53b78f1 build: number: 0 From 589a465458c7c199d44b560515d00e4b4825228d Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 21:34:04 -0400 Subject: [PATCH 32/81] Update locityper to 0.15.3 (#47773) --- recipes/locityper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/locityper/meta.yaml b/recipes/locityper/meta.yaml index fc0b74ded328a5..d21617ca451115 100644 --- a/recipes/locityper/meta.yaml +++ b/recipes/locityper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "locityper" %} -{% set version = "0.15.2" %} +{% set version = "0.15.3" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://github.com/tprodanov/locityper/archive/refs/tags/v{{ version }}.tar.gz - sha256: e3c76264fc55d448cf8dc12e4610d2b30241eae23718fe1a3a1229ef6d224c8d + sha256: bf123a391b08a6ab5bcb642f93af30bce021dffc82bcca37555c5657f209ceee build: number: 0 From 6263cfb35cbff0c8a168ae87be023b61e09e4d26 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 21:34:21 -0400 Subject: [PATCH 33/81] Update vcfdist to 2.5.2 (#47776) --- recipes/vcfdist/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vcfdist/meta.yaml b/recipes/vcfdist/meta.yaml index 7936d92329652e..791f3bdcbb03e6 100644 --- a/recipes/vcfdist/meta.yaml +++ b/recipes/vcfdist/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.5.1" %} -{% set sha256 = "25d7d8c8613cfcfb1c582edbe09d20d1d3cb7de6fd6d18c0b83ac4d8195637a3" %} +{% set version = "2.5.2" %} +{% set sha256 = "c0c7ef16df051755234a13f2a5316f7963ccaf5d06c588c16838febaa839bbe1" %} package: name: vcfdist From 4321c45b6f34a66f1703b13a39b66f1be8dec303 Mon Sep 17 00:00:00 2001 From: Martin Larralde Date: Thu, 9 May 2024 03:35:46 +0200 Subject: [PATCH 34/81] Update `pyopal` to `v0.6.0` (#47778) --- recipes/pyopal/meta.yaml | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/recipes/pyopal/meta.yaml b/recipes/pyopal/meta.yaml index 12f3680ab55a12..c93eec8a306266 100644 --- a/recipes/pyopal/meta.yaml +++ b/recipes/pyopal/meta.yaml @@ -1,5 +1,5 @@ {% set name = "pyopal" %} -{% set version = "0.5.2" %} +{% set version = "0.6.0" %} package: name: "{{ name|lower }}" @@ -7,7 +7,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: c58b573890a13197caea03d25b7db1de6fd8f8ece91b1337ab96c7b1668616c9 + sha256: 434875e92be7bee2c27b7034f502f263ef777b364349a5fd50ec07d7401d1915 build: number: 0 @@ -25,10 +25,12 @@ requirements: - pip - cython - setuptools + - scoring-matrices >=0.2 run: - python - setuptools - archspec + - scoring-matrices >=0.2 test: imports: @@ -46,3 +48,5 @@ about: extra: recipe-maintainers: - althonos + additional-platforms: + - linux-aarch64 From c2aaf9235e2f4fe96bd5f538da6c531f6b223970 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Florian=20Plaza=20O=C3=B1ate?= <4588656+fplazaonate@users.noreply.github.com> Date: Thu, 9 May 2024 03:39:23 +0200 Subject: [PATCH 35/81] Update kmer-jellyfish (#47708) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Add python bindings * Update build version * clean up recipe * edit meta.yaml * edit build.sh * Run tests * Disable python bindings on OSX --------- Co-authored-by: Florian Plaza Oñate Co-authored-by: mencian --- recipes/kmer-jellyfish/build.sh | 17 ++++++++++++++--- recipes/kmer-jellyfish/meta.yaml | 27 +++++++++++++++------------ 2 files changed, 29 insertions(+), 15 deletions(-) diff --git a/recipes/kmer-jellyfish/build.sh b/recipes/kmer-jellyfish/build.sh index 071a68120b44c5..423caa66311f44 100644 --- a/recipes/kmer-jellyfish/build.sh +++ b/recipes/kmer-jellyfish/build.sh @@ -1,5 +1,16 @@ -#!/bin/bash +#!/bin/bash -euo -./configure --prefix=$PREFIX -make -j 4 +if [[ "$OSTYPE" == "darwin"* ]]; then + # Python bindings do no work on OSX + ./configure --prefix=${PREFIX} --with-sse CXX="${CXX}" \ + CXXFLAGS="${CXXFLAGS} -O3" CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \ + LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +else + ./configure --prefix=${PREFIX} --enable-python-binding --with-sse CXX="${CXX}" \ + CXXFLAGS="${CXXFLAGS} -O3" CPPFLAGS="${CPPFLAGS} -I${PREFIX}/include" \ + LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +fi + +make -j ${CPU_COUNT} +make check -j ${CPU_COUNT} make install diff --git a/recipes/kmer-jellyfish/meta.yaml b/recipes/kmer-jellyfish/meta.yaml index 9d58c7c727f833..3abc6d73d93e49 100644 --- a/recipes/kmer-jellyfish/meta.yaml +++ b/recipes/kmer-jellyfish/meta.yaml @@ -1,35 +1,38 @@ +{% set name = "kmer-jellyfish" %} {% set version = "2.3.1" %} package: - name: kmer-jellyfish + name: {{ name }} version: {{ version }} -build: - number: 0 - run_exports: - - {{ pin_subpackage("kmer-jellyfish", max_pin="2.3.1") }} - source: url: https://github.com/gmarcais/Jellyfish/releases/download/v{{ version }}/jellyfish-{{ version }}.tar.gz sha256: ee032b57257948ca0f0610883099267572c91a635eecbd88ae5d8974c2430fcd +build: + number: 1 + run_exports: + - {{ pin_subpackage("kmer-jellyfish", max_pin="x") }} + requirements: build: - - make - {{ compiler('cxx') }} + - make test: commands: - jellyfish --version 2>&1 > /dev/null about: - home: http://www.genome.umd.edu/jellyfish.html - license: GPL-3.0 - license_family: GPL - summary: Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence - dev_url: https://github.com/gmarcais/Jellyfish + home: "https://genome.umd.edu/jellyfish.html" + license: "GPL-3.0-or-later" + license_family: GPL3 + summary: "Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence." + dev_url: "https://github.com/gmarcais/Jellyfish" + doc_url: "https://genome.umd.edu/docs/JellyfishUserGuide.pdf" extra: identifiers: - biotools:jellyfish - doi:10.1093/bioinformatics/btr011 + - usegalaxy-eu:jellyfish From 6f2d3d7b124f0a1ae736b200d23558af7efea9a6 Mon Sep 17 00:00:00 2001 From: vpepe Date: Wed, 8 May 2024 21:41:19 -0400 Subject: [PATCH 36/81] Update seqverify to v1.2.0 (#47775) * Update meta.yaml * Update build.sh * Update meta.yaml --- recipes/seqverify/build.sh | 1 + recipes/seqverify/meta.yaml | 7 ++++--- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/seqverify/build.sh b/recipes/seqverify/build.sh index 7b4d20d3e9b983..d264f97e6ebe07 100644 --- a/recipes/seqverify/build.sh +++ b/recipes/seqverify/build.sh @@ -6,5 +6,6 @@ cp seqverify $PREFIX/bin cp seqver_functions.py $PREFIX/bin cp seqver_plots.py $PREFIX/bin cp seqver_lofFinder.py $PREFIX/bin +cp seqver_gtf.py $PREFIX/bin cp seqver_genomeupdate.py $PREFIX/bin diff --git a/recipes/seqverify/meta.yaml b/recipes/seqverify/meta.yaml index f43ed2d87bda82..3d6b1a1c25d436 100644 --- a/recipes/seqverify/meta.yaml +++ b/recipes/seqverify/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} package: name: seqverify version: {{ version }} source: - url: https://github.com/mpiersonsmela/SeqVerify/archive/refs/tags/v1.1.0.tar.gz - sha256: d6d9b1fc56bc7f7263d99d3e4f13e12a0e5ed0894c1ba70397805c46b5d34ec2 + url: https://github.com/mpiersonsmela/SeqVerify/archive/refs/tags/v1.2.0.tar.gz + sha256: 9ebdb2f48b0a55d5821e094a73064a96c6e8b4ae5bef54b17bf2f9e21c33f193 build: noarch: generic @@ -23,6 +23,7 @@ requirements: - htslib - idna - igv =2.13.2 + - igv-reports - kraken2 - matplotlib-base - numpy From b7d94e1c6d4ff8fe3192b01e9548e883cf20d946 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 9 May 2024 04:54:53 +0300 Subject: [PATCH 37/81] Add Linux aarch64 build for more Bioconductor packages (#47756) - acme - affy - biocneighbors - msstats - multtest - rbgl - rgraphviz Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bioconductor-acme/meta.yaml | 6 ++++-- recipes/bioconductor-affy/meta.yaml | 6 ++++-- recipes/bioconductor-biocneighbors/meta.yaml | 11 ++++++++--- recipes/bioconductor-msstats/meta.yaml | 4 +++- recipes/bioconductor-multtest/meta.yaml | 6 ++++-- recipes/bioconductor-rbgl/meta.yaml | 4 +++- recipes/bioconductor-rgraphviz/meta.yaml | 8 +++++++- 7 files changed, 33 insertions(+), 12 deletions(-) diff --git a/recipes/bioconductor-acme/meta.yaml b/recipes/bioconductor-acme/meta.yaml index 1a43fedf235017..47fd7e89692ed6 100644 --- a/recipes/bioconductor-acme/meta.yaml +++ b/recipes/bioconductor-acme/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6668a82e0a26ac03c9697e2cf22eb75e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -37,11 +37,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'GPL-3-only' summary: 'Algorithms for Calculating Microarray Enrichment (ACME)' description: 'ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:acme parent_recipe: diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml index b6cfed74b149d5..d7bd0340a6b273 100644 --- a/recipes/bioconductor-affy/meta.yaml +++ b/recipes/bioconductor-affy/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 09376016b32f86f707ff9b8f8cb8a1a5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -47,11 +47,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.0)' + license: 'LGPL-3-only' summary: 'Methods for Affymetrix Oligonucleotide Arrays' description: 'The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. ''affy'' is fully functional without it.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:affy parent_recipe: diff --git a/recipes/bioconductor-biocneighbors/meta.yaml b/recipes/bioconductor-biocneighbors/meta.yaml index 83929f7284c5ae..ed7fc9a00824d4 100644 --- a/recipes/bioconductor-biocneighbors/meta.yaml +++ b/recipes/bioconductor-biocneighbors/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3cfb96ab6d42068c5b875fa6fcefd779 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -46,8 +46,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3-only summary: 'Nearest Neighbor Detection for Bioconductor Packages' description: 'Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Exact searches can be performed using the k-means for k-nearest neighbors algorithm or with vantage point trees. Approximate searches can be performed using the Annoy or HNSW libraries. Searching on either Euclidean or Manhattan distances is supported. Parallelization is achieved for all methods by using BiocParallel. Functions are also provided to search for all neighbors within a given distance.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' - +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + - usegalaxy-eu:{{ name|lower }} diff --git a/recipes/bioconductor-msstats/meta.yaml b/recipes/bioconductor-msstats/meta.yaml index e17bbdfaade327..16e7cd6050d080 100644 --- a/recipes/bioconductor-msstats/meta.yaml +++ b/recipes/bioconductor-msstats/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: fac3a495f2e627a75b10a9b941d3674d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -69,6 +69,8 @@ about: summary: 'Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments' description: 'A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:msstats parent_recipe: diff --git a/recipes/bioconductor-multtest/meta.yaml b/recipes/bioconductor-multtest/meta.yaml index 2921e8d93355a4..9a08836c831301 100644 --- a/recipes/bioconductor-multtest/meta.yaml +++ b/recipes/bioconductor-multtest/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 7d81a8460781f4a86f01a9df5fcf50d7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -42,11 +42,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL + license: LGPL-3-only summary: 'Resampling-based multiple hypothesis testing' description: 'Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:multtest - doi:10.1007/0-387-29362-0_15 diff --git a/recipes/bioconductor-rbgl/meta.yaml b/recipes/bioconductor-rbgl/meta.yaml index f201a7627ea36c..6dea29c5ac9ad2 100644 --- a/recipes/bioconductor-rbgl/meta.yaml +++ b/recipes/bioconductor-rbgl/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a18b5ad5c49f058b6f65a2bd0a4274d1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -43,6 +43,8 @@ about: summary: 'An interface to the BOOST graph library' description: 'A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:rbgl - doi:10.1093/bioinformatics/bth458 diff --git a/recipes/bioconductor-rgraphviz/meta.yaml b/recipes/bioconductor-rgraphviz/meta.yaml index d28bc09c5210b1..299076f3c8b84c 100644 --- a/recipes/bioconductor-rgraphviz/meta.yaml +++ b/recipes/bioconductor-rgraphviz/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: b93e5d1c383b1e5cd06e4dec89a43ce8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -42,4 +42,10 @@ about: license: EPL summary: 'Provides plotting capabilities for R graph objects' description: 'Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + - usegalaxy-eu:{{ name|lower }} From 446523a4d70954126088acbc7550a73eba47448b Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 9 May 2024 04:55:11 +0300 Subject: [PATCH 38/81] Add Linux aarch64 build for more Bioconductor packages (#47757) - biocc - cohcap - copa - ebarrays - flowcore - mscoreutils - mzr - pcamethods Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bioconductor-bioqc/meta.yaml | 6 ++++-- recipes/bioconductor-cohcap/meta.yaml | 6 ++++-- recipes/bioconductor-copa/meta.yaml | 8 +++++++- recipes/bioconductor-ebarrays/meta.yaml | 6 ++++-- recipes/bioconductor-flowcore/meta.yaml | 4 +++- recipes/bioconductor-mscoreutils/meta.yaml | 9 ++++++++- recipes/bioconductor-mzr/meta.yaml | 4 +++- recipes/bioconductor-pcamethods/meta.yaml | 6 ++++-- 8 files changed, 37 insertions(+), 12 deletions(-) diff --git a/recipes/bioconductor-bioqc/meta.yaml b/recipes/bioconductor-bioqc/meta.yaml index 1a1c3267230517..857cec979ea61b 100644 --- a/recipes/bioconductor-bioqc/meta.yaml +++ b/recipes/bioconductor-bioqc/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9e9b338e001fdeb614091e4fa0cf50cd build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -41,11 +41,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=3) + file LICENSE' + license: 'GPL-3.0-or-later + file LICENSE' summary: 'Detect tissue heterogeneity in expression profiles with gene sets' description: 'BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.' license_file: LICENSE extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:bioqc - doi:10.1186/s12864-017-3661-2 diff --git a/recipes/bioconductor-cohcap/meta.yaml b/recipes/bioconductor-cohcap/meta.yaml index eaafa323c174fe..6e92de0db88031 100644 --- a/recipes/bioconductor-cohcap/meta.yaml +++ b/recipes/bioconductor-cohcap/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6c7c601f8c8aee626d2fa1a6dd306dca build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -51,11 +51,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3.0-only summary: 'CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data' description: 'COHCAP (pronounced "co-cap") provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options. Discussion Group: https://sourceforge.net/p/cohcap/discussion/bioconductor/' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:cohcap parent_recipe: diff --git a/recipes/bioconductor-copa/meta.yaml b/recipes/bioconductor-copa/meta.yaml index a06e57133a6756..4c51fca6b76879 100644 --- a/recipes/bioconductor-copa/meta.yaml +++ b/recipes/bioconductor-copa/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: bd372714a4dd7e70b90d9232fcba322d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -40,3 +40,9 @@ about: summary: 'Functions to perform cancer outlier profile analysis.' description: 'COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + - usegalaxy-eu:{{ name|lower }} diff --git a/recipes/bioconductor-ebarrays/meta.yaml b/recipes/bioconductor-ebarrays/meta.yaml index c4b790998b5de0..54575ad557b040 100644 --- a/recipes/bioconductor-ebarrays/meta.yaml +++ b/recipes/bioconductor-ebarrays/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: d273e2e9411207653d4e079e14484026 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -39,11 +39,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'GPL-3.0-or-later' summary: 'Unified Approach for Simultaneous Gene Clustering and Differential Expression Identification' description: 'EBarrays provides tools for the analysis of replicated/unreplicated microarray data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:ebarrays - doi:10.1111/j.1541-0420.2006.00611.x diff --git a/recipes/bioconductor-flowcore/meta.yaml b/recipes/bioconductor-flowcore/meta.yaml index bb31c70c0c63a2..f5a254a4c935c5 100644 --- a/recipes/bioconductor-flowcore/meta.yaml +++ b/recipes/bioconductor-flowcore/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3b0696fd3fc45a87531ab3503be00277 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -58,6 +58,8 @@ about: summary: 'flowCore: Basic structures for flow cytometry data' description: 'Provides S4 data structures and basic functions to deal with flow cytometry data.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:flowcore - doi:10.1186/1471-2105-10-106 diff --git a/recipes/bioconductor-mscoreutils/meta.yaml b/recipes/bioconductor-mscoreutils/meta.yaml index abc01147f991f3..e3dad78d9e43e7 100644 --- a/recipes/bioconductor-mscoreutils/meta.yaml +++ b/recipes/bioconductor-mscoreutils/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 163cc129bc77ed033c124fed5bf7d9ca build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -47,3 +47,10 @@ about: summary: 'Core Utils for Mass Spectrometry Data' description: 'MsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning), quantitative aggregation functions (median polish, robust summarisation, ...), missing data imputation, data normalisation (quantiles, vsn, ...) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + - usegalaxy-eu:{{ name|lower }} + diff --git a/recipes/bioconductor-mzr/meta.yaml b/recipes/bioconductor-mzr/meta.yaml index 788afdea54a79a..9a63146869b814 100644 --- a/recipes/bioconductor-mzr/meta.yaml +++ b/recipes/bioconductor-mzr/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: aae8b88db5fd49675b653b861702800e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -53,6 +53,8 @@ about: summary: 'parser for netCDF, mzXML, mzData and mzML and mzIdentML files (mass spectrometry data)' description: 'mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:mzr parent_recipe: diff --git a/recipes/bioconductor-pcamethods/meta.yaml b/recipes/bioconductor-pcamethods/meta.yaml index daa71eb6ce8894..a206627ebca748 100644 --- a/recipes/bioconductor-pcamethods/meta.yaml +++ b/recipes/bioconductor-pcamethods/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a989ad925a9852f55eb5e4d16d1529d0 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -44,11 +44,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 3)' + license: 'GPL-3.0-or-later' summary: 'A collection of PCA methods' description: 'Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:pcamethods - doi:10.1093/bioinformatics/btm069 From 33151f75fc21a0eb82d15bc16a34138be3c1045e Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 9 May 2024 04:57:45 +0300 Subject: [PATCH 39/81] Add Linux aarch64 build for more Bioconductor packages (#47758) - dirichletmultinomial - geneselectmmd - ibmq - maftools - martini - methylmnm Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bioconductor-dirichletmultinomial/meta.yaml | 6 ++++-- recipes/bioconductor-geneselectmmd/meta.yaml | 10 ++++++++-- recipes/bioconductor-ibmq/meta.yaml | 8 +++++++- recipes/bioconductor-maftools/meta.yaml | 7 ++++++- recipes/bioconductor-martini/meta.yaml | 11 +++++++++-- recipes/bioconductor-methylmnm/meta.yaml | 6 ++++-- 6 files changed, 38 insertions(+), 10 deletions(-) diff --git a/recipes/bioconductor-dirichletmultinomial/meta.yaml b/recipes/bioconductor-dirichletmultinomial/meta.yaml index c522f169f78524..94f6743365b396 100644 --- a/recipes/bioconductor-dirichletmultinomial/meta.yaml +++ b/recipes/bioconductor-dirichletmultinomial/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8527c543b1ada9640d2f434fb516ff4e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -43,11 +43,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: LGPL-3 + license: LGPL-3.0-only summary: 'Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data' description: 'Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:dirichletmultinomial - doi:10.1371/journal.pone.0030126 diff --git a/recipes/bioconductor-geneselectmmd/meta.yaml b/recipes/bioconductor-geneselectmmd/meta.yaml index ca852645683200..f28cf53ec6c7b6 100644 --- a/recipes/bioconductor-geneselectmmd/meta.yaml +++ b/recipes/bioconductor-geneselectmmd/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: dd6cd07bbe095fca03ce4b134c1507b8 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -41,8 +41,14 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'GPL-3.0-or-later' summary: 'Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions' description: 'Gene selection based on a mixture of marginal distributions.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + - usegalaxy-eu:{{ name|lower }} diff --git a/recipes/bioconductor-ibmq/meta.yaml b/recipes/bioconductor-ibmq/meta.yaml index 4633abf58f473b..e1827d81263052 100644 --- a/recipes/bioconductor-ibmq/meta.yaml +++ b/recipes/bioconductor-ibmq/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9737c0aee38670491b2f29f73dcb743c build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -45,3 +45,9 @@ about: summary: 'integrated Bayesian Modeling of eQTL data' description: 'integrated Bayesian Modeling of eQTL data' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + - usegalaxy-eu:{{ name|lower }} diff --git a/recipes/bioconductor-maftools/meta.yaml b/recipes/bioconductor-maftools/meta.yaml index 45bb7956998034..ef10236192193d 100644 --- a/recipes/bioconductor-maftools/meta.yaml +++ b/recipes/bioconductor-maftools/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 3dadc2b7f6f1693ae23a41b61f541db4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -52,6 +52,11 @@ about: description: 'Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.' license_file: LICENSE extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + - usegalaxy-eu:{{ name|lower }} parent_recipe: name: bioconductor-maftools path: recipes/bioconductor-maftools diff --git a/recipes/bioconductor-martini/meta.yaml b/recipes/bioconductor-martini/meta.yaml index 707dd1d27a6ae7..59fd53e07ccc9c 100644 --- a/recipes/bioconductor-martini/meta.yaml +++ b/recipes/bioconductor-martini/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 85e3366daf7ac24c0f50261fafe8b274 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -47,8 +47,15 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3.0-only summary: 'GWAS Incorporating Networks' description: 'martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + - usegalaxy-eu:{{ name|lower }} + diff --git a/recipes/bioconductor-methylmnm/meta.yaml b/recipes/bioconductor-methylmnm/meta.yaml index 86b480b3cdd61d..ffae70e36fd4aa 100644 --- a/recipes/bioconductor-methylmnm/meta.yaml +++ b/recipes/bioconductor-methylmnm/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 3d6c83c4fa30daea5b1c91e70f67c6b5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -37,11 +37,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3.0-only summary: 'detect different methylation level (DMR)' description: 'To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:methylmnm - doi:10.1101/gr.156539.113 From f4e2ca4fe2429bc63c0d535fc8f84e823e5a712f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 22:04:40 -0400 Subject: [PATCH 40/81] Update gseapy to 1.1.3 (#47774) * Update gseapy to 1.1.3 * Update meta.yaml --------- Co-authored-by: Christian Brueffer --- recipes/gseapy/meta.yaml | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index c2470c14e26197..80f4af5e7a0e31 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -1,10 +1,10 @@ package: name: gseapy - version: "1.1.2" + version: "1.1.3" source: - url: https://files.pythonhosted.org/packages/bc/54/4e09f7d74d0d1778b081fff8853a3ca6d03a951032424691be6d2df6fbea/gseapy-1.1.2.tar.gz - sha256: fd861b9e75a5103bd4a6bd67925f8f4a3c5b48d51e0ae068f56fb01aa9201e9e + url: https://files.pythonhosted.org/packages/28/c2/7c03f74682de640b71ba9a9958c5c8a90867b0f4f9ffef2c15702113d47a/gseapy-1.1.3.tar.gz + sha256: 7f9218bb4014a862680d4d3e806e59bec8f81601e876a04495922da81da1b395 build: entry_points: @@ -12,7 +12,7 @@ build: run_exports: - {{ pin_subpackage("gseapy", max_pin="x") }} skip: True # [py2k or py == 36 ] - number: 1 + number: 0 requirements: build: @@ -40,9 +40,10 @@ test: about: home: https://github.com/zqfang/gseapy - license: MIT License + license: MIT summary: 'Gene Set Enrichment Analysis in Python' license_family: MIT + license_file: LICENSE extra: additional-platforms: From 98c06c2119ecbb614deea2a396022f0a1ec46c2e Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 9 May 2024 05:11:20 +0300 Subject: [PATCH 41/81] minimap2: add linux-aarch64 build (#46432) * minimap2: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov * Pass ARM64 specific options to minimap2's make to use sse2neon Signed-off-by: Martin Tzvetanov Grigorov * Apply the improvements from #47753 Try without passing $INCLUDES Signed-off-by: Martin Tzvetanov Grigorov * minimap2: Patch the Makefile so that it is possible to override variables and later append to them Signed-off-by: Martin Tzvetanov Grigorov * minimap2: Pass -I${PREFIX}/include to CFLAGS, so that it applies to sdust too Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/minimap2/build.sh | 27 ++++++++++++++----- recipes/minimap2/meta.yaml | 26 +++++++++++++----- recipes/minimap2/override-makefile.patch | 34 ++++++++++++++++++++++++ 3 files changed, 74 insertions(+), 13 deletions(-) create mode 100644 recipes/minimap2/override-makefile.patch diff --git a/recipes/minimap2/build.sh b/recipes/minimap2/build.sh index 61715a5671d739..b6f518c35e81ba 100644 --- a/recipes/minimap2/build.sh +++ b/recipes/minimap2/build.sh @@ -1,11 +1,24 @@ #!/bin/bash -mkdir -p $PREFIX/bin $PREFIX/lib $PREFIX/include +set -xe -export CPATH=${PREFIX}/include +mkdir -p ${PREFIX}/bin ${PREFIX}/lib ${PREFIX}/include -make INCLUDES="-I$PREFIX/include" CFLAGS="-g -Wall -O2 -Wc++-compat -L$PREFIX/lib" minimap2 sdust -cp minimap2 misc/paftools.js $PREFIX/bin -cp sdust $PREFIX/bin -cp libminimap2.a $PREFIX/lib -cp *.h $PREFIX/include +case $(uname -m) in + aarch64) + ARCH_OPTS="aarch64=1" + ;; + *) + ARCH_OPTS="" + ;; +esac + +make CFLAGS="-g -Wall -O2 -Wc++-compat -I${PREFIX}/include -L${PREFIX}/lib" \ + ${ARCH_OPTS} -j${CPU_COUNT} minimap2 sdust + +chmod 755 minimap2 && chmod 755 sdust + +cp minimap2 misc/paftools.js ${PREFIX}/bin +cp sdust ${PREFIX}/bin +cp libminimap2.a ${PREFIX}/lib +cp *.h ${PREFIX}/include diff --git a/recipes/minimap2/meta.yaml b/recipes/minimap2/meta.yaml index 8962090b3324bf..7c2bc89fb15209 100644 --- a/recipes/minimap2/meta.yaml +++ b/recipes/minimap2/meta.yaml @@ -1,17 +1,20 @@ +{% set name = "minimap2" %} {% set version = "2.28" %} package: - name: minimap2 + name: {{ name }} version: {{ version }} source: - url: https://github.com/lh3/minimap2/archive/v{{ version }}.tar.gz + url: https://github.com/lh3/{{ name }}/archive/v{{ version }}.tar.gz sha256: 5ea6683b4184b5c49f6dbaef2bc5b66155e405888a0790d1b21fd3c93e474278 + patches: + - override-makefile.patch build: - number: 0 + number: 1 run_exports: - - {{ pin_subpackage('minimap2', max_pin="x") }} + - {{ pin_subpackage(name, max_pin="x") }} requirements: build: @@ -32,7 +35,18 @@ test: - test -e $PREFIX/include/minimap.h about: - home: https://github.com/lh3/minimap2 + home: "https://github.com/lh3/minimap2" license: MIT - license_file: LICENSE.txt + license_family: MIT + license_file: "LICENSE.txt" summary: 'A versatile pairwise aligner for genomic and spliced nucleotide sequences.' + dev_url: "https://github.com/lh3/minimap2" + doc_url: "https://lh3.github.io/minimap2/minimap2.html" + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name| lower }} + - usegalaxy-eu:{{ name| lower }} + - doi:10.1093/bioinformatics/bty191 \ No newline at end of file diff --git a/recipes/minimap2/override-makefile.patch b/recipes/minimap2/override-makefile.patch new file mode 100644 index 00000000000000..154fb53273159a --- /dev/null +++ b/recipes/minimap2/override-makefile.patch @@ -0,0 +1,34 @@ +diff --git i/Makefile w/Makefile +index 17b13b6..f0767c8 100644 +--- i/Makefile ++++ w/Makefile +@@ -20,22 +20,22 @@ else # if sse2only is defined + endif + else # if arm_neon is defined + OBJS+=ksw2_extz2_neon.o ksw2_extd2_neon.o ksw2_exts2_neon.o +- INCLUDES+=-Isse2neon ++ override INCLUDES+=-Isse2neon + ifeq ($(aarch64),) #if aarch64 is not defined +- CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char ++ override CFLAGS+=-D_FILE_OFFSET_BITS=64 -mfpu=neon -fsigned-char + else #if aarch64 is defined +- CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char ++ override CFLAGS+=-D_FILE_OFFSET_BITS=64 -fsigned-char + endif + endif + + ifneq ($(asan),) +- CFLAGS+=-fsanitize=address +- LIBS+=-fsanitize=address -ldl ++ override CFLAGS+=-fsanitize=address ++ override LIBS+=-fsanitize=address -ldl + endif + + ifneq ($(tsan),) +- CFLAGS+=-fsanitize=thread +- LIBS+=-fsanitize=thread -ldl ++ override CFLAGS+=-fsanitize=thread ++ override LIBS+=-fsanitize=thread -ldl + endif + + .PHONY:all extra clean depend From 1091f71d4f5d1107c5ab8a2ab6aca48072167297 Mon Sep 17 00:00:00 2001 From: Andrey Prjibelski Date: Thu, 9 May 2024 05:41:42 +0300 Subject: [PATCH 42/81] Update IsoQuant to 3.4.0 (#47779) * Update IsoQuant to 3.4.0 * add run_exports and license details * add pyyaml * clean up recipe --------- Co-authored-by: mencian Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/isoquant/build.sh | 2 +- recipes/isoquant/meta.yaml | 28 ++++++++++++++++++++-------- 2 files changed, 21 insertions(+), 9 deletions(-) diff --git a/recipes/isoquant/build.sh b/recipes/isoquant/build.sh index 8736b04c39060a..47cdaa0e478ac5 100644 --- a/recipes/isoquant/build.sh +++ b/recipes/isoquant/build.sh @@ -6,4 +6,4 @@ mkdir -p $PREFIX/bin chmod a+x *.py cp -rp * "$OUTDIR/" cd $PREFIX/bin -ln -s "../${OUTDIR#$PREFIX}"/*.py . +ln -sf "../${OUTDIR#$PREFIX}"/*.py . diff --git a/recipes/isoquant/meta.yaml b/recipes/isoquant/meta.yaml index 9d46f8b5da8548..dd0aa4b29118f6 100644 --- a/recipes/isoquant/meta.yaml +++ b/recipes/isoquant/meta.yaml @@ -1,6 +1,6 @@ {% set name = "IsoQuant" %} -{% set version = "3.3.1" %} -{% set sha256 = "1d0f7d4c3f42f48ab6cd30fef8e743a60032a8c36cee15ed0de4df21c847fde2" %} +{% set version = "3.4.0" %} +{% set sha256 = "acf040b9f8ddec3aa51b5c151e556e65acf8fa227d0242eda804a09d2ba06702" %} package: name: {{ name | lower }} @@ -13,19 +13,23 @@ source: build: number: 0 noarch: generic + run_exports: + - {{ pin_subpackage('isoquant', max_pin='x') }} requirements: run: - - python >=3.7 + - python >=3.8 - argcomplete >=1.11.1 - argh >=0.26.2 - biopython >=1.76 - gffutils >=0.10.1 - minimap2 >=2.18 - - pandas >=1.0 + - packaging + - pandas >=1.0.1 - pybedtools >=0.8.1 - - pyfaidx >=0.5.8 + - pyfaidx >=0.7 - pysam >=0.15 + - pyyaml >=5.4 - samtools >=1.14 - simplejson >=3.17.0 - six >=1.14.0 @@ -38,6 +42,14 @@ test: - rm -rf isoquant_test about: - summary: IsoQuant is a tool for reference-based analysis of long RNA reads, such as gene/transcript quantification and discovery. - home: https://github.com/ablab/IsoQuant - license: GPL2 + summary: "IsoQuant is a tool for reference-based analysis of long RNA reads, such as gene/transcript quantification and discovery." + home: "https://github.com/ablab/IsoQuant" + license: "GPL-2.0-or-later" + license_family: GPL2 + license_file: LICENSE + dev_url: "https://github.com/ablab/IsoQuant" + doc_url: "https://github.com/ablab/IsoQuant/blob/master/README.md" + +extra: + identifiers: + - doi:10.1038/s41587-022-01565-y From d617f54e20d8f6d3ee4fd4680175a09c377ed0e9 Mon Sep 17 00:00:00 2001 From: wjunLu <135617475+wjunLu@users.noreply.github.com> Date: Thu, 9 May 2024 10:42:32 +0800 Subject: [PATCH 43/81] Add build for yaggo (#47782) * Add aarch64 build for yaggo * Fix bug --- build-fail-blacklist | 1 - recipes/yaggo/meta.yaml | 4 +++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index b2af9f3218d265..d97aaf77986678 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -95,7 +95,6 @@ recipes/workspace recipes/wtforms-alchemy recipes/wtforms-components recipes/xmlbuilder -recipes/yaggo # the following packages have open PRs labeled with "Move to conda-forge" recipes/perl-alien-build diff --git a/recipes/yaggo/meta.yaml b/recipes/yaggo/meta.yaml index 335fb1eff35342..a800d0084bca4b 100644 --- a/recipes/yaggo/meta.yaml +++ b/recipes/yaggo/meta.yaml @@ -7,7 +7,9 @@ package: build: noarch: generic - number: 0 + number: 1 + run_exports: + - {{ pin_subpackage("yaggo", max_pin='x.x') }} source: url: https://github.com/gmarcais/yaggo/releases/download/v{{version}}/yaggo From cd7a78285b8f4ce4d1d82b0fd7e1ae66636c71b5 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 8 May 2024 23:38:30 -0400 Subject: [PATCH 44/81] Update hmftools-mark-dups to 1.1.6 (#47783) --- recipes/hmftools-mark-dups/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-mark-dups/meta.yaml b/recipes/hmftools-mark-dups/meta.yaml index b3a5ae8fd6f73c..d976fe5e2671d6 100644 --- a/recipes/hmftools-mark-dups/meta.yaml +++ b/recipes/hmftools-mark-dups/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "1.1.5" %} -{% set sha256 = "59cc87f1e7923b11d5c1b59c3c8fb531ace6d5d39dac61a165d76b4d1c472c10" %} +{% set version = "1.1.6" %} +{% set sha256 = "417f58daa7dd5fd51328173e6fda1e72fdbe55cb6868ad999671e039a62b2732" %} package: name: hmftools-mark-dups From 743559dd48de7926e0ae2a56064c12d038ac9a57 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 May 2024 00:00:34 -0400 Subject: [PATCH 45/81] Update fairy to 0.5.4 (#47784) --- recipes/fairy/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fairy/meta.yaml b/recipes/fairy/meta.yaml index 068a0072ee13f7..691ea5e2997ae2 100644 --- a/recipes/fairy/meta.yaml +++ b/recipes/fairy/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.5.3" %} +{% set version = "0.5.4" %} package: name: fairy @@ -11,7 +11,7 @@ build: source: url: https://github.com/bluenote-1577/fairy/archive/v{{ version }}.tar.gz - sha256: 8a949dde81a89b8c6f7bea74e793d90df923b34addd360448263a129977771e8 + sha256: ea76f8ea428e0413db98b7feb9becaf1ce1824ca49f62e20a7371d00ac6d89ff requirements: build: From 9a7a5b80f96d866bec341a03ed4a1be13ad48189 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 May 2024 00:53:57 -0400 Subject: [PATCH 46/81] Update sdeper to 1.3.0 (#47785) --- recipes/sdeper/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/sdeper/meta.yaml b/recipes/sdeper/meta.yaml index c8c79fd5403546..3ac11f91ac0f96 100755 --- a/recipes/sdeper/meta.yaml +++ b/recipes/sdeper/meta.yaml @@ -1,6 +1,6 @@ # This is the recipe file to publish SDePER to Bioconda {% set name = "sdeper" %} -{% set version = "1.2.1" %} +{% set version = "1.3.0" %} package: name: "{{ name|lower }}" @@ -8,7 +8,7 @@ package: source: url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz" - sha256: d46f8002662466e9b86533267648d525bb8ceaa1ade49cc175779d5c7c3c8ab2 + sha256: 539621f0cca35c04e70a27c330af4b192b7d72babd6288c24e976b60edd5f052 build: number: 0 From e8b006de0885eb8071cb4e8f67ecd884a6b761c1 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 May 2024 02:24:04 -0400 Subject: [PATCH 47/81] Update hybpiper to 2.1.7 (#47786) * Update hybpiper to 2.1.7 * add run_exports * add run_exports --------- Co-authored-by: mencian --- recipes/hybpiper/build.sh | 3 - recipes/hybpiper/build_failure.osx-64.yaml | 104 ------------------ recipes/hybpiper/meta.yaml | 37 ++++--- .../sorted_nearest/build_failure.osx-64.yaml | 104 ------------------ 4 files changed, 20 insertions(+), 228 deletions(-) delete mode 100644 recipes/hybpiper/build.sh delete mode 100644 recipes/hybpiper/build_failure.osx-64.yaml delete mode 100644 recipes/sorted_nearest/build_failure.osx-64.yaml diff --git a/recipes/hybpiper/build.sh b/recipes/hybpiper/build.sh deleted file mode 100644 index 9354bfd059e95d..00000000000000 --- a/recipes/hybpiper/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -# Install HybPiper -$PYTHON -m pip install --no-deps --ignore-installed . - diff --git a/recipes/hybpiper/build_failure.osx-64.yaml b/recipes/hybpiper/build_failure.osx-64.yaml deleted file mode 100644 index 49cc73ed6a35e9..00000000000000 --- a/recipes/hybpiper/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 35ef1b5ef27a3fde696e04cc087c0ade7814653834908273028c6dee9080552e # The commit at which this recipe failed to build. -skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |2- - ld64_osx-64: 609-h8ce0179_13 conda-forge - libclang-cpp15: 15.0.7-default_hdb78580_2 conda-forge - libcxx: 16.0.4-hd57cbcb_0 conda-forge - libexpat: 2.5.0-hf0c8a7f_1 conda-forge - libffi: 3.4.2-h0d85af4_5 conda-forge - libiconv: 1.17-hac89ed1_0 conda-forge - libllvm15: 15.0.7-he4b1e75_2 conda-forge - libsqlite: 3.42.0-h58db7d2_0 conda-forge - libxml2: 2.11.4-hd95e348_0 conda-forge - libzlib: 1.2.13-hfd90126_4 conda-forge - llvm-tools: 15.0.7-he4b1e75_2 conda-forge - ncurses: 6.3-h96cf925_1 conda-forge - openssl: 3.1.1-h8a1eda9_1 conda-forge - python: 3.11.3-h99528f9_0_cpython conda-forge - readline: 8.2-h9e318b2_1 conda-forge - setuptools: 67.7.2-pyhd8ed1ab_0 conda-forge - sigtool: 0.1.3-h88f4db0_0 conda-forge - tapi: 1100.0.11-h9ce4665_0 conda-forge - tk: 8.6.12-h5dbffcc_0 conda-forge - tzdata: 2023c-h71feb2d_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - zstd: 1.5.2-hbc0c0cd_6 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Source cache directory is: /opt/mambaforge/envs/bioconda/conda-bld/src_cache - INFO:conda_build.source:Downloading source to cache: v2.1.3_677d046ceb.tar.gz - INFO:conda_build.source:Downloading https://github.com/mossmatters/HybPiper/archive/refs/tags/v2.1.3.tar.gz - Downloading source to cache: v2.1.3_677d046ceb.tar.gz - Downloading https://github.com/mossmatters/HybPiper/archive/refs/tags/v2.1.3.tar.gz - Success - INFO:conda_build.source:Success - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/hybpiper_1685527655123/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hybpiper_1685527655123/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/hybpiper_1685527655123/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/hybpiper_1685527655123/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hybpiper-2.1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/hybpiper-2.1.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-pie -headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - /opt/mambaforge/envs/bioconda/conda-bld/hybpiper_1685527655123/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/bin/python: No module named pip - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in - sys.exit(main()) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main - call_conda_build(action, config) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build - result = api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build - return build_tree( - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree - packages_from_this = build(metadata, stats, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build - utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env, - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/hybpiper_1685527655123/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/hybpiper/meta.yaml b/recipes/hybpiper/meta.yaml index af8c4ee099aa56..6c54f977823e50 100644 --- a/recipes/hybpiper/meta.yaml +++ b/recipes/hybpiper/meta.yaml @@ -1,5 +1,5 @@ {% set name = "hybpiper" %} -{% set version = "2.1.6" %} +{% set version = "2.1.7" %} package: name: {{ name|lower }} @@ -7,18 +7,21 @@ package: source: url: "https://github.com/mossmatters/HybPiper/archive/refs/tags/v{{ version }}.tar.gz" - sha256: ac175b2b02cd9fcc1d195a4edd68dd1e004c6d2e2bb5658f4cce9b2a4339b4c9 + sha256: 5532767bb92a524f97ef05808cba39090e034ab3e1d48c5307ed812d3909b018 build: number: 0 + noarch: python + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + entry_points: + - hybpiper = hybpiper.assemble:main + run_exports: + - {{ pin_subpackage('hybpiper', max_pin="x") }} requirements: - build: - - {{ compiler('c') }} - - setuptools host: - - python >=3.7.0 # [linux] - - python >=3.7.0,<3.10 # [osx] + - python >=3.7 + - pip run: - bbmap >=38.44 - biopython >=1.80 @@ -34,9 +37,9 @@ requirements: - progressbar2 >=3.38.0 - psutil >=5.9.0 - samtools >=1.14 - - seaborn >=0.11.1 - - spades >=3.15.2 # [osx] - - spades >=3.15.4 # [linux] + - seaborn-base >=0.11.1 + - spades >=3.15.2 # [osx] + - spades >=3.15.4 # [linux] - trimmomatic test: @@ -55,10 +58,10 @@ test: - hybpiper.fix_targetfile about: - home: "https://github.com/mossmatters/HybPiper" - license: GPL-3.0-or-later - license_family: GPL - license_file: LICENSE.txt - summary: > - HybPiper is a suite of Python scripts/modules for targeted sequence - capture + home: "https://github.com/mossmatters/HybPiper" + dev_url: "https://github.com/mossmatters/HybPiper" + doc_url: "https://github.com/mossmatters/HybPiper/wiki" + license: "GPL-3.0-or-later" + license_family: GPL3 + license_file: "LICENSE.txt" + summary: "HybPiper is a suite of Python scripts/modules for targeted sequence capture." diff --git a/recipes/sorted_nearest/build_failure.osx-64.yaml b/recipes/sorted_nearest/build_failure.osx-64.yaml deleted file mode 100644 index 7c08d5d09c2e9e..00000000000000 --- a/recipes/sorted_nearest/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: aa8b08221fa8e68e1a02f7e6ff820b2afd94c1811832b9422de23482d8c27295 # The commit at which this recipe failed to build. -skiplist: false # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above. -log: |- - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #2 - {} is not a Mach-O file - Can't parse the binary at the index #3 - {} is not a Mach-O file - Can't parse the binary at the index #4 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - {} is not a Mach-O file - Can't parse the binary at the index #2 - {} is not a Mach-O file - Can't parse the binary at the index #3 - {} is not a Mach-O file - Can't parse the binary at the index #4 - {} is not a Mach-O file - Can't parse the binary at the index #0 - {} is not a Mach-O file - Can't parse the binary at the index #1 - INFO: sysroot: '/System/Library/Frameworks/' files: '['vmnet.framework/Versions/A/_CodeSignature/CodeResources', 'vmnet.framework/Versions/A/Resources/version.plist', 'vmnet.framework/Versions/A/Resources/en.lproj/InfoPlist.strings', 'vmnet.framework/Versions/A/Resources/Info.plist']' - INFO: sysroot: '/usr/lib/' files: '['zsh/5.8.1/zsh/zselect.so', 'zsh/5.8.1/zsh/zpty.so', 'zsh/5.8.1/zsh/zprof.so', 'zsh/5.8.1/zsh/zleparameter.so']' - INFO: sysroot: '/opt/X11/' files: '[]' - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/k_nearest.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/merge_by.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/cluster_by.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/tiles.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/introns.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/k_nearest_ties.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/windows.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/max_disjoint_intervals.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/clusters.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/annotate_clusters.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - INFO (sorted_nearest,lib/python3.8/site-packages/sorted_nearest/src/sorted_nearest.cpython-38-darwin.so): Needed DSO /System/Library/Frameworks/libSystem.B.dylib found in $SYSROOT - WARNING (sorted_nearest): interpreter (Python) package conda-forge::python-3.8.17-hf9b03c3_0_cpython in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to build/ignore_run_exports) - Fixing permissions - INFO :: Time taken to mark (prefix) - 0 replacements in 0 files was 0.20 seconds - TEST START: /opt/mambaforge/envs/bioconda/conda-bld/osx-64/sorted_nearest-0.0.39-py38h604ca31_0.tar.bz2 - Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/work' to '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/work_moved_sorted_nearest-0.0.39-py38h604ca31_0_osx-64' - shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/work_moved_sorted_nearest-0.0.39-py38h604ca31_0_osx-64) - INFO:conda_build.utils:Renaming work directory '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/work' to '/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/work_moved_sorted_nearest-0.0.39-py38h604ca31_0_osx-64' - INFO:conda_build.utils:shutil.move(work)=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/work, dest=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/work_moved_sorted_nearest-0.0.39-py38h604ca31_0_osx-64) - Reloading output folder: /opt/mambaforge/envs/bioconda/conda-bld - - ## Package Plan ## - - environment location: /opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - - - The following NEW packages will be INSTALLED: - - bzip2: 1.0.8-h0d85af4_4 conda-forge - ca-certificates: 2023.5.7-h8857fd0_0 conda-forge - libblas: 3.9.0-17_osx64_openblas conda-forge - libcblas: 3.9.0-17_osx64_openblas conda-forge - libcxx: 16.0.6-hd57cbcb_0 conda-forge - libffi: 3.4.2-h0d85af4_5 conda-forge - libgfortran: 5.0.0-11_3_0_h97931a8_31 conda-forge - libgfortran5: 12.2.0-he409387_31 conda-forge - liblapack: 3.9.0-17_osx64_openblas conda-forge - libopenblas: 0.3.23-openmp_h429af6e_0 conda-forge - libsqlite: 3.42.0-h58db7d2_0 conda-forge - libzlib: 1.2.13-h8a1eda9_5 conda-forge - llvm-openmp: 16.0.6-hff08bdf_0 conda-forge - ncurses: 6.4-hf0c8a7f_0 conda-forge - numpy: 1.24.4-py38h9a4a08f_0 conda-forge - openssl: 3.1.1-h8a1eda9_1 conda-forge - python: 3.8.17-hf9b03c3_0_cpython conda-forge - python_abi: 3.8-3_cp38 conda-forge - readline: 8.2-h9e318b2_1 conda-forge - sorted_nearest: 0.0.39-py38h604ca31_0 local - tk: 8.6.12-h5dbffcc_0 conda-forge - xz: 5.2.6-h775f41a_0 conda-forge - - Preparing transaction: ...working... done - Verifying transaction: ...working... done - Executing transaction: ...working... done - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/test_tmp - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/test_tmp/run_test.py", line 2, in - import sorted_nearest - File "/opt/mambaforge/envs/bioconda/conda-bld/sorted_nearest_1688764114444/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib/python3.8/site-packages/sorted_nearest/__init__.py", line 1, in - import: 'sorted_nearest' - import pkg_resources - ModuleNotFoundError: No module named 'pkg_resources' - Tests failed for sorted_nearest-0.0.39-py38h604ca31_0.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken - WARNING:conda_build.build:Tests failed for sorted_nearest-0.0.39-py38h604ca31_0.tar.bz2 - moving package to /opt/mambaforge/envs/bioconda/conda-bld/broken - TESTS FAILED: sorted_nearest-0.0.39-py38h604ca31_0.tar.bz2 -# Last 100 lines of the build log. From e6eac07468163c02377fd2c3595ad3e1e124a389 Mon Sep 17 00:00:00 2001 From: Ryota Wagatsuma <42291982+TsumaR@users.noreply.github.com> Date: Thu, 9 May 2024 18:16:41 +0900 Subject: [PATCH 48/81] Add vclean (#47545) * Add vclean * Change test in vclean * Change test in vclean * Change test in vclean * edit for lin * test * use spdx identifiers --------- Co-authored-by: TsumaR --- recipes/vclean/meta.yaml | 53 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 recipes/vclean/meta.yaml diff --git a/recipes/vclean/meta.yaml b/recipes/vclean/meta.yaml new file mode 100644 index 00000000000000..d70333f25020c2 --- /dev/null +++ b/recipes/vclean/meta.yaml @@ -0,0 +1,53 @@ +{% set name = "vclean" %} +{% set version = "0.0.2" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/vclean-{{ version }}.tar.gz + sha256: 3624ccf7b8160af1584cc7fa99b7036fb81818a1941b9fd31729ce85c48cce73 + +build: + entry_points: + - vclean = vclean.cli:cli + noarch: python + script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation + number: 0 + run_exports: + - {{ pin_subpackage("vclean", max_pin="x") }} + +requirements: + host: + - python >=3.9 + - flit-core >=3.2,<4 + - pip + run: + - python >=3.9 + - pandas + - numpy + - matplotlib-base + - seaborn + - scikit-learn + - lightgbm + - biopython + - checkv + - seqkit + - kmer-jellyfish + - prodigal + - mmseqs2 + +test: + commands: + - vclean --help + +about: + summary: 'vClean: Assessing the contamination of viral genomes' + home: https://github.com/TsumaR/vclean + license: GPL-3.0-only + license_file: LICENSE + +extra: + recipe-maintainers: + - TsumaR From 0a55466072d8eba73c587e0f98da4331d2fc9ace Mon Sep 17 00:00:00 2001 From: Ryan Morrison <54183277+ryanmorrison22@users.noreply.github.com> Date: Thu, 9 May 2024 15:45:47 +0100 Subject: [PATCH 49/81] Update KPop (#47559) * Add dependency for newer bash versions * Bump up build number --------- Co-authored-by: Ryan Morrison --- recipes/kpop/meta.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/kpop/meta.yaml b/recipes/kpop/meta.yaml index 2ed264f8d134b5..2c715ea857c7e3 100644 --- a/recipes/kpop/meta.yaml +++ b/recipes/kpop/meta.yaml @@ -16,10 +16,11 @@ source: build: run_exports: - {{ pin_subpackage(name, max_pin="x") }} - number: 0 + number: 1 requirements: run: + - bash >=4.4.20 - r-data.table - r-ca From 286a67025ba73be67fdbb73899ceafb06eaaf598 Mon Sep 17 00:00:00 2001 From: Amine Ghozlane Date: Thu, 9 May 2024 16:46:23 +0200 Subject: [PATCH 50/81] Update Meteor 2.0.11 (#47793) * Add meteor recipe * Fix meteor testing according to bioconda azure deployment system * Fix shasum * Update recipes/meteor/meta.yaml Co-authored-by: Thanh Lee * Update recipes/meteor/meta.yaml Co-authored-by: Thanh Lee * Update recipes/meteor/meta.yaml Co-authored-by: Thanh Lee * Update to meteor 2.0.11 --------- Co-authored-by: Thanh Lee --- recipes/meteor/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/meteor/meta.yaml b/recipes/meteor/meta.yaml index 154327b4de91ca..0490c8b54121bc 100644 --- a/recipes/meteor/meta.yaml +++ b/recipes/meteor/meta.yaml @@ -1,5 +1,5 @@ {% set name = "meteor" %} -{% set version = "2.0.9" %} +{% set version = "2.0.11" %} package: name: {{ name }} @@ -8,7 +8,7 @@ package: source: url: https://github.com/metagenopolis/meteor/archive/{{ version }}.tar.gz - sha256: e828010c5dd52e04156f6f0263d9d2635831d1253df9a5e0dc47becbd8e45c43 + sha256: 2e6119f2a3b19227ef6a9ed990dbbfebd2d47144cf032d0d410f015541e7b1fe build: noarch: python From c574b70420bb1574dbe638b48d02fd99d9adf630 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Thu, 9 May 2024 17:47:59 +0300 Subject: [PATCH 51/81] Add Linux aarch64 build for more Bioconductor packages (#47787) - acgh - bluster - ebcoexpress - flowclust - flowmatch - gaga - vsn Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bioconductor-acgh/meta.yaml | 6 ++++-- recipes/bioconductor-bluster/meta.yaml | 9 +++++++-- recipes/bioconductor-ebcoexpress/meta.yaml | 10 ++++++++-- recipes/bioconductor-flowclust/meta.yaml | 8 +++++++- recipes/bioconductor-flowmatch/meta.yaml | 4 +++- recipes/bioconductor-gaga/meta.yaml | 6 ++++-- recipes/bioconductor-vsn/meta.yaml | 4 +++- 7 files changed, 36 insertions(+), 11 deletions(-) diff --git a/recipes/bioconductor-acgh/meta.yaml b/recipes/bioconductor-acgh/meta.yaml index ce96cf84127e51..480a44e57a5219 100644 --- a/recipes/bioconductor-acgh/meta.yaml +++ b/recipes/bioconductor-acgh/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 137af76dc5756a83094da18eb0bededa build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -42,11 +42,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 + license: GPL-2.0-only summary: 'Classes and functions for Array Comparative Genomic Hybridization data' description: 'Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:acgh - doi:10.1093/bioinformatics/bti677 diff --git a/recipes/bioconductor-bluster/meta.yaml b/recipes/bioconductor-bluster/meta.yaml index 2ba7e0232e16b2..672e737816913d 100644 --- a/recipes/bioconductor-bluster/meta.yaml +++ b/recipes/bioconductor-bluster/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: baf91e0700b1f49eb80522be9eb8204d build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -50,8 +50,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3.0-only summary: 'Clustering Algorithms for Bioconductor' description: 'Wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-ebcoexpress/meta.yaml b/recipes/bioconductor-ebcoexpress/meta.yaml index f22be4d02c7b70..e9424815f0a43f 100644 --- a/recipes/bioconductor-ebcoexpress/meta.yaml +++ b/recipes/bioconductor-ebcoexpress/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 66fa4257fbd0222064b30f6c15e74ab1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -40,8 +40,14 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'GPL-3.0-or-later' summary: 'EBcoexpress for Differential Co-Expression Analysis' description: 'An Empirical Bayesian Approach to Differential Co-Expression Analysis at the Gene-Pair Level' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + diff --git a/recipes/bioconductor-flowclust/meta.yaml b/recipes/bioconductor-flowclust/meta.yaml index 946cfdb1cd4144..e23f51ab272d9d 100644 --- a/recipes/bioconductor-flowclust/meta.yaml +++ b/recipes/bioconductor-flowclust/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 50e5d774ae44b8aaca69069733c175e3 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -48,3 +48,9 @@ about: summary: 'Clustering for Flow Cytometry' description: 'Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: ''consult the README file available in the inst directory of the source distribution for necessary configuration instructions''.' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + diff --git a/recipes/bioconductor-flowmatch/meta.yaml b/recipes/bioconductor-flowmatch/meta.yaml index fbbc71e016972a..c27636b543ddd3 100644 --- a/recipes/bioconductor-flowmatch/meta.yaml +++ b/recipes/bioconductor-flowmatch/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 78b2b9dc87eec35dbc65c59dadb1ffd9 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -45,6 +45,8 @@ about: summary: 'Matching and meta-clustering in flow cytometry' description: 'Matching cell populations and building meta-clusters and templates from a collection of FC samples.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:flowmatch - doi:10.1038/nmeth.3252 diff --git a/recipes/bioconductor-gaga/meta.yaml b/recipes/bioconductor-gaga/meta.yaml index e96e988b0e6644..929fa49e04c277 100644 --- a/recipes/bioconductor-gaga/meta.yaml +++ b/recipes/bioconductor-gaga/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d1b404912b9a23365c9085dc91e20a10 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -41,11 +41,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'GPL-3.0-or-later' summary: 'GaGa hierarchical model for high-throughput data analysis' description: 'Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package).' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:gaga - doi:10.1214/09-aoas244 diff --git a/recipes/bioconductor-vsn/meta.yaml b/recipes/bioconductor-vsn/meta.yaml index f9f993fd76b958..073be9e2252d48 100644 --- a/recipes/bioconductor-vsn/meta.yaml +++ b/recipes/bioconductor-vsn/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 1c9484f361b22f76135af5567306f0c6 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -48,6 +48,8 @@ about: summary: 'Variance stabilization and calibration for microarray data' description: 'The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:vsn parent_recipe: From 35b228ad5b03a5e0a50e128df8fcaa2e75f6a3ee Mon Sep 17 00:00:00 2001 From: zhenxian <920596906@qq.com> Date: Fri, 10 May 2024 01:17:53 +0800 Subject: [PATCH 52/81] Update meta.yaml (#47797) --- recipes/clair3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/clair3/meta.yaml b/recipes/clair3/meta.yaml index 946dd4d1d77374..d16a9e72fa7d1d 100644 --- a/recipes/clair3/meta.yaml +++ b/recipes/clair3/meta.yaml @@ -7,10 +7,10 @@ package: source: url: http://www.bio8.cs.hku.hk/clair3/bioconda/Clair3_v{{ version }}.zip - sha256: c0bd4441e844e9319c914515a7727b38eefacea31848236eb4c31e4517f087bb + sha256: 3bc493269878af0d06c3fa006656d77ab01ae55d19c217fcf2ba1d68e2350a9d build: - number: 0 + number: 1 skip: True # [osx] run_exports: - {{ pin_subpackage(name, max_pin="x") }} From bf7981121c791c7aac3661c5d4b4581169b9bd85 Mon Sep 17 00:00:00 2001 From: stuber Date: Thu, 9 May 2024 14:51:31 -0600 Subject: [PATCH 53/81] vsnp3 version 3.21 (#47805) --- recipes/vsnp3/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/vsnp3/meta.yaml b/recipes/vsnp3/meta.yaml index 2e02a9566043cb..8e7303c87efc2f 100644 --- a/recipes/vsnp3/meta.yaml +++ b/recipes/vsnp3/meta.yaml @@ -1,7 +1,7 @@ {% set user = "USDA-VS" %} {% set name = "vsnp3" %} -{% set version = "3.20" %} -{% set sha256 = "cb255d9e5381dcfe516bc92e35ecd3735b5447bfae74323392462579997c7a77" %} +{% set version = "3.21" %} +{% set sha256 = "5bb49fb4a26b80c6cb49652eb2fec5c16ffb57c71eddb0942074bcdeb2d93e99" %} package: name: {{ name|lower }} From 85fc16cb7b7df190491115cb08bbadd461ccde05 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 May 2024 21:17:19 -0400 Subject: [PATCH 54/81] Update isoquant to 3.4.1 (#47809) --- recipes/isoquant/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/isoquant/meta.yaml b/recipes/isoquant/meta.yaml index dd0aa4b29118f6..0d7b27eeb72ffa 100644 --- a/recipes/isoquant/meta.yaml +++ b/recipes/isoquant/meta.yaml @@ -1,6 +1,6 @@ {% set name = "IsoQuant" %} -{% set version = "3.4.0" %} -{% set sha256 = "acf040b9f8ddec3aa51b5c151e556e65acf8fa227d0242eda804a09d2ba06702" %} +{% set version = "3.4.1" %} +{% set sha256 = "a2e9d80da36567ab64647b60a919e78c69da7d61d0e9436f1682acada7841485" %} package: name: {{ name | lower }} From 1b0632809f9831178f787617f4d12a1582e15213 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 May 2024 21:17:29 -0400 Subject: [PATCH 55/81] Update kalamari to 5.5.0 (#47811) --- recipes/kalamari/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/kalamari/meta.yaml b/recipes/kalamari/meta.yaml index 93dae4a9a96e0c..7604fbed6b8421 100644 --- a/recipes/kalamari/meta.yaml +++ b/recipes/kalamari/meta.yaml @@ -1,5 +1,5 @@ {% set name = "Kalamari" %} -{% set version = "5.4.1" %} +{% set version = "5.5.0" %} package: name: {{ name|lower }} @@ -7,10 +7,10 @@ package: source: url: https://github.com/lskatz/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz - sha256: 587c2e59c9961f3900baafb9d1c5c49cc0554976417ee9a46d6c8cd7c63e22c5 + sha256: 6d55a1d0c3dcefb8a4933165974652cf58ac6b5eff52aa6031a799402a85e5ee build: - number: 1 + number: 0 noarch: generic run_exports: - {{ pin_subpackage(name|lower, max_pin="x") }} From e21909f21ab91cb8ad6ab79cbf4d92268db4e150 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 May 2024 21:20:14 -0400 Subject: [PATCH 56/81] Update allo to 1.1.1 (#47808) --- recipes/allo/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/allo/meta.yaml b/recipes/allo/meta.yaml index 22ff8c5d8ce4ef..286f0f2b467902 100644 --- a/recipes/allo/meta.yaml +++ b/recipes/allo/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "1.0.5" %} +{% set version = "1.1.1" %} package: name: allo version: {{ version }} source: - url: https://files.pythonhosted.org/packages/45/65/e52455e8c4edb3bf93cb2b429f22ea36f54f2e6e21fe2789967d08cc390e/bio-allo-1.0.5.tar.gz - sha256: 0834fce916e3523af3e06c4c713f549c89cb846e08e3b74fe75cef4ad53dea26 + url: https://files.pythonhosted.org/packages/3d/03/0206bf7d3bd24fe7bc03ff9570e93db3b4255eb3cd7dce1606f4be6c37cf/bio_allo-1.1.1.tar.gz + sha256: b72bcbd900965e8b2fbbc17b174b44a8938994a4aeb8d532fb6f6a52b115b69e build: run_exports: From f19bef6271cca1f3707e0321c54b1b4293075294 Mon Sep 17 00:00:00 2001 From: Milot Mirdita Date: Fri, 10 May 2024 10:34:45 +0900 Subject: [PATCH 57/81] Update Foldseek to 9-427df8a (#47802) --- recipes/foldseek/meta.yaml | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/recipes/foldseek/meta.yaml b/recipes/foldseek/meta.yaml index 7c189ec2f96287..6b7f4cfe4bef30 100644 --- a/recipes/foldseek/meta.yaml +++ b/recipes/foldseek/meta.yaml @@ -1,12 +1,12 @@ -{% set version = "8-ef4e960" %} -{% set sha256 = "c74d02c4924d20275cc567783b56fff10e76ed67f3d642f53c283f67c4180a1e" %} +{% set version = "9-427df8a" %} +{% set sha256 = "b17d2d85b49a8508f79ffd8b15e54afc5feef5f3fb0276a291141ca5dbbbe8bc" %} package: name: foldseek version: {{ version|replace("-", ".") }} build: - number: 1 + number: 0 run_exports: - {{ pin_subpackage('foldseek', max_pin="x") }} @@ -49,9 +49,11 @@ about: extra: identifiers: - doi:10.1038/s41587-023-01773-0 + - doi:10.1038/s41586-023-06510-w + - doi:10.1101/2024.04.14.589414 - biotools:foldseek recipe-maintainers: - milot-mirdita - martin-steinegger additional-platforms: - - linux-aarch64 \ No newline at end of file + - linux-aarch64 From 6c24db69f8e14f26011f99dbafbfc6f0e9d97fdc Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 May 2024 21:40:51 -0400 Subject: [PATCH 58/81] Update hmftools-sage to 3.4.3 (#47812) --- recipes/hmftools-sage/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/hmftools-sage/meta.yaml b/recipes/hmftools-sage/meta.yaml index 8fe36d68487734..61982d00288419 100644 --- a/recipes/hmftools-sage/meta.yaml +++ b/recipes/hmftools-sage/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "3.4.2" %} -{% set sha256 = "10cf12b1fb8782ad44898fb7ac1e413dc8f9eec3448ae31d03effbd4e01ccc03" %} +{% set version = "3.4.3" %} +{% set sha256 = "bf5c0369ab7449915826c2ba726ed07bd9883c90965919971b5f4dc1ef3684fd" %} package: name: hmftools-sage From 318b3649972736b2f0361b1ab41fc5daf2a2b62a Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 10 May 2024 04:44:45 +0300 Subject: [PATCH 59/81] Add Linux aarch64 build for more Bioconductor packages (#47790) * Add Linux aarch64 build for more Bioconductor packages - csar - decipher - dmrcaller - fastseg - kebabs - msa - seqarray Signed-off-by: Martin Tzvetanov Grigorov * Update bioconductor-seqarray to 1.42.4. Hoping that it builds on Mac OSX Signed-off-by: Martin Tzvetanov Grigorov * Fix a typo in property name Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bioconductor-csar/meta.yaml | 7 ++++++- recipes/bioconductor-decipher/meta.yaml | 6 ++++-- recipes/bioconductor-dmrcaller/meta.yaml | 10 ++++++++-- recipes/bioconductor-fastseg/meta.yaml | 6 ++++-- recipes/bioconductor-kebabs/meta.yaml | 8 ++++++-- recipes/bioconductor-msa/meta.yaml | 7 ++++++- recipes/bioconductor-seqarray/meta.yaml | 14 ++++++++++---- 7 files changed, 44 insertions(+), 14 deletions(-) diff --git a/recipes/bioconductor-csar/meta.yaml b/recipes/bioconductor-csar/meta.yaml index 4767cf2e78ac2c..8a7ab11fb87da5 100644 --- a/recipes/bioconductor-csar/meta.yaml +++ b/recipes/bioconductor-csar/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: cf22689abca527406f9f2b333739d7bc build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -46,3 +46,8 @@ about: summary: 'Statistical tools for the analysis of ChIP-seq data' description: 'Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-decipher/meta.yaml b/recipes/bioconductor-decipher/meta.yaml index 257e0cf8b5364e..32250e45f32800 100644 --- a/recipes/bioconductor-decipher/meta.yaml +++ b/recipes/bioconductor-decipher/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 0a32c782d61a604dc3594c684daa8c75 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -45,11 +45,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3.0-only summary: 'Tools for curating, analyzing, and manipulating biological sequences' description: 'A toolset for deciphering and managing biological sequences.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:DECIPHER parent_recipe: diff --git a/recipes/bioconductor-dmrcaller/meta.yaml b/recipes/bioconductor-dmrcaller/meta.yaml index 877d463affcbd6..a58fdd462be2df 100644 --- a/recipes/bioconductor-dmrcaller/meta.yaml +++ b/recipes/bioconductor-dmrcaller/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 1c5b37620b4950eb63e32c3063235e8e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -46,8 +46,14 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3.0-only summary: 'Differentially Methylated Regions caller' description: 'Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + diff --git a/recipes/bioconductor-fastseg/meta.yaml b/recipes/bioconductor-fastseg/meta.yaml index 2a67786842c05a..5e6686b13d3d21 100644 --- a/recipes/bioconductor-fastseg/meta.yaml +++ b/recipes/bioconductor-fastseg/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ca8ead071a9b881b19dea7b71e0e73b4 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -45,11 +45,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'LGPL (>= 2.0)' + license: 'LGPL-3.0-or-later' summary: 'fastseg - a fast segmentation algorithm' description: 'fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments'' first and higher order moments.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/LGPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:fastseg parent_recipe: diff --git a/recipes/bioconductor-kebabs/meta.yaml b/recipes/bioconductor-kebabs/meta.yaml index d3fae5cd61e11e..5543552572b654 100644 --- a/recipes/bioconductor-kebabs/meta.yaml +++ b/recipes/bioconductor-kebabs/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: d6c4a16d9fd157b1e68acc8d4816017e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -55,11 +55,15 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2.1)' + license: 'GPL-3.0-or-later' summary: 'Kernel-Based Analysis Of Biological Sequences' description: 'The package provides functionality for kernel-based analysis of DNA, RNA, and amino acid sequences via SVM-based methods. As core functionality, kebabs implements following sequence kernels: spectrum kernel, mismatch kernel, gappy pair kernel, and motif kernel. Apart from an efficient implementation of standard position-independent functionality, the kernels are extended in a novel way to take the position of patterns into account for the similarity measure. Because of the flexibility of the kernel formulation, other kernels like the weighted degree kernel or the shifted weighted degree kernel with constant weighting of positions are included as special cases. An annotation-specific variant of the kernels uses annotation information placed along the sequence together with the patterns in the sequence. The package allows for the generation of a kernel matrix or an explicit feature representation in dense or sparse format for all available kernels which can be used with methods implemented in other R packages. With focus on SVM-based methods, kebabs provides a framework which simplifies the usage of existing SVM implementations in kernlab, e1071, and LiblineaR. Binary and multi-class classification as well as regression tasks can be used in a unified way without having to deal with the different functions, parameters, and formats of the selected SVM. As support for choosing hyperparameters, the package provides cross validation - including grouped cross validation, grid search and model selection functions. For easier biological interpretation of the results, the package computes feature weights for all SVMs and prediction profiles which show the contribution of individual sequence positions to the prediction result and indicate the relevance of sequence sections for the learning result and the underlying biological functions.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} parent_recipe: name: bioconductor-kebabs path: recipes/bioconductor-kebabs diff --git a/recipes/bioconductor-msa/meta.yaml b/recipes/bioconductor-msa/meta.yaml index d7f02314603889..3b02f9e8d1d8f7 100644 --- a/recipes/bioconductor-msa/meta.yaml +++ b/recipes/bioconductor-msa/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 78eba41452ffe497e1a7c72116335b3e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -52,3 +52,8 @@ about: description: 'The ''msa'' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-seqarray/meta.yaml b/recipes/bioconductor-seqarray/meta.yaml index 189913b7b1e3e2..c533d2b4768d9a 100644 --- a/recipes/bioconductor-seqarray/meta.yaml +++ b/recipes/bioconductor-seqarray/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.42.0" %} +{% set version = "1.42.4" %} {% set name = "SeqArray" %} {% set bioc = "3.18" %} @@ -11,9 +11,9 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - md5: 9754225574380705e505629db229d41a + md5: 607951cd78bea8ef1156be7aba41052f build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -47,8 +47,14 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3.0-only summary: 'Data Management of Large-Scale Whole-Genome Sequence Variant Calls' description: 'Data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + From 1ee8513aaa5095c7e33bbc992be370264199ff4e Mon Sep 17 00:00:00 2001 From: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Date: Thu, 9 May 2024 21:26:06 -0500 Subject: [PATCH 60/81] Add recipe for LIQA v1.2.0 (#47813) --- recipes/liqa/meta.yaml | 51 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 recipes/liqa/meta.yaml diff --git a/recipes/liqa/meta.yaml b/recipes/liqa/meta.yaml new file mode 100644 index 00000000000000..d7514f6f116c0c --- /dev/null +++ b/recipes/liqa/meta.yaml @@ -0,0 +1,51 @@ +{% set name = "liqa" %} +{% set version = "1.3.4" %} + +package: + name: {{ name|lower }} + version: {{ version }} + +source: + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/liqa-{{ version }}.tar.gz + sha256: f8b2e6f0226d99f513d17be3758e6b3e2e9b7b40579f840d28737e827358850e + +build: + number: 0 + noarch: python + entry_points: + - liqa=liqa_src.liqa:main + script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir + run_exports: + - {{ pin_subpackage('liqa', max_pin="x") }} + +requirements: + host: + - python >=3 + - pip + run: + - python >=3 + - lifelines + - numpy + - pysam + - scipy + - r-base + - r-betareg + +test: + imports: + - liqa_src + commands: + - liqa --help + +about: + home: "https://github.com/WGLab/LIQA" + summary: "A statistical tool to quantify isoform-specific expression using long-read RNA-seq." + license: MIT + license_family: MIT + license_file: LICENSE + dev_url: "https://github.com/WGLab/LIQA" + doc_url: "https://github.com/WGLab/LIQA/blob/master/doc/Usage.md" + +extra: + identifiers: + - doi:10.1186/s13059-021-02399-8 From 71b6caca64f1a43b2bbc2ab5088df2cfdb9dd913 Mon Sep 17 00:00:00 2001 From: Lexi Morrissey <46540607+anmorrissey@users.noreply.github.com> Date: Thu, 9 May 2024 22:26:19 -0400 Subject: [PATCH 61/81] Update meta.yaml (#47807) * Update meta.yaml * clean up recipe --------- Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> Co-authored-by: mencian --- recipes/allo/meta.yaml | 19 +++++++++++-------- 1 file changed, 11 insertions(+), 8 deletions(-) diff --git a/recipes/allo/meta.yaml b/recipes/allo/meta.yaml index 286f0f2b467902..3fa7b1a6eed240 100644 --- a/recipes/allo/meta.yaml +++ b/recipes/allo/meta.yaml @@ -1,26 +1,27 @@ +{% set name = "allo" %} {% set version = "1.1.1" %} package: - name: allo + name: {{ name }} version: {{ version }} source: - url: https://files.pythonhosted.org/packages/3d/03/0206bf7d3bd24fe7bc03ff9570e93db3b4255eb3cd7dce1606f4be6c37cf/bio_allo-1.1.1.tar.gz + url: https://pypi.io/packages/source/b/bio-{{ name }}/bio_allo-{{ version }}.tar.gz sha256: b72bcbd900965e8b2fbbc17b174b44a8938994a4aeb8d532fb6f6a52b115b69e build: run_exports: - {{ pin_subpackage('allo', max_pin="x") }} - number: 0 + number: 1 noarch: python - script: {{ PYTHON }} -m pip install . -vv + script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv requirements: host: - pip - - python >=3.8 + - python >=3.10 run: - - python >=3.8 + - python >=3.10 - numpy - joblib - tensorflow >=2.11 @@ -31,10 +32,12 @@ test: - allo --help about: - home: https://github.com/seqcode/allo + home: "https://github.com/seqcode/allo" license: MIT - license_file: LICENSE.txt + license_family: MIT + license_file: "LICENSE.txt" summary: "Multi-mapped read rescue strategy for gene regulatory analyses" + dev_url: "https://github.com/seqcode/allo" extra: recipe-maintainers: From 0b2eda893b9e19dcee8346128919d7013039cc65 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Thu, 9 May 2024 22:26:49 -0400 Subject: [PATCH 62/81] Update ebcsgen to 2.2.0 (#47801) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Update ebcsgen to 2.2.0 * Update meta.yaml (#47803) --------- Co-authored-by: Matej Troják --- recipes/ebcsgen/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/ebcsgen/meta.yaml b/recipes/ebcsgen/meta.yaml index 959dead71e109d..8b7c3b2d211b35 100644 --- a/recipes/ebcsgen/meta.yaml +++ b/recipes/ebcsgen/meta.yaml @@ -1,5 +1,5 @@ {% set name = "eBCSgen" %} -{% set version = "2.1.0" %} +{% set version = "2.2.0" %} package: name: {{ name|lower }} @@ -7,12 +7,14 @@ package: source: url: "https://github.com/sybila/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz" - sha256: 604cac3facc314c01778102ab0285cdc2cdbb75edb8289a6e7cac28e820f0e2a + sha256: 023e2a0a3613ab36e9344d07e589f483283b306be9b760b4827b0807781b0743 build: number: 0 noarch: python script: {{ PYTHON }} -m pip install . --ignore-installed --no-deps -vv + run_exports: + - {{ pin_subpackage('ebcsgen', max_pin="x.x") }} requirements: host: From c73676d8859ec6f487876d7d054cd8b9af401c44 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 10 May 2024 05:10:10 +0200 Subject: [PATCH 63/81] bump nf-core 2.14.1 (#47798) * bump nf-core 2.14.1 * Update meta.yaml --------- Co-authored-by: Nils Homer --- recipes/nf-core/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/nf-core/meta.yaml b/recipes/nf-core/meta.yaml index ac60d3bce94fbd..c40ef0900f5f00 100644 --- a/recipes/nf-core/meta.yaml +++ b/recipes/nf-core/meta.yaml @@ -1,13 +1,13 @@ {% set name = "nf-core" %} -{% set version = "2.13.1" %} -{% set sha256 = "297bb52144a0651b3b718325726b10a14bef0b1b3a1d65a0eadb4badb47c8a6f" %} +{% set version = "2.14.1" %} +{% set sha256 = "35bd8d73ecca4eb87443fada31bc7b2562429de3a4bfbf7261db348d14bf54bb" %} package: name: {{ name|lower }} version: {{ version }} source: - url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/nf_core-{{ version }}.tar.gz sha256: '{{ sha256 }}' build: From 47db42c96109239d00f38f168ddce6edbfdfc43b Mon Sep 17 00:00:00 2001 From: bolduc Date: Thu, 9 May 2024 23:14:14 -0400 Subject: [PATCH 64/81] Add vcontact3 (#47673) * Initial commit * Attempt to fix TreeStyle via pip * Attempt to fix TreeStyle via pip round 2 * Attempt to fix TreeStyle but not exclude it... * Attempt to fix TreeStyle with correct script command * Attempt to fix TreeStyle with dependencies * Adjusting optional package as optional in source --- recipes/vcontact3/meta.yaml | 62 +++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 recipes/vcontact3/meta.yaml diff --git a/recipes/vcontact3/meta.yaml b/recipes/vcontact3/meta.yaml new file mode 100644 index 00000000000000..7fe1af8435c228 --- /dev/null +++ b/recipes/vcontact3/meta.yaml @@ -0,0 +1,62 @@ +{% set name = "vcontact3" %} +{% set version = "3.0.0.b38" %} + +package: + name: "{{ name|lower }}" + version: "{{ version }}" + +source: + url: "https://bitbucket.org/MAVERICLab/vcontact3/get/{{ version }}.tar.gz" + sha256: fc56f0c3ae4d3016287e4ab9ad86847b089e7c8eca78fa393fe8eba965c182fc + +build: + number: 0 + noarch: python + run_exports: + - {{ pin_subpackage('vcontact3', max_pin='x') }} + script: "{{ PYTHON }} -m pip install --no-deps ." + +requirements: + host: + - pip + - python >=3.9,<3.11 + run: + - python >=3.9,<3.11 + - numpy >=1.23.5 + - pandas >=2.1.1 + - scikit-learn >=1.2.2 + - seaborn >=0.12.1 + - matplotlib-base >=3.7.1 + - scipy >=1.10.1 + - jenkspy >=0.3.2 + - networkx >=3.1 + - upsetplot >=0.7.0 + - tqdm >=4.65.0 + - ete3 >=3.1.3 + - jinja2 >=3.0.3 + - scikit-bio >=0.5.8 + - pyrodigal >=2.3.0 + - pyrodigal-gv >=0.3.1 + - joblib >=1.2.0 + - python-igraph >=0.10.4 + - psutil >=5.9.5 + - biopython >=1.81 + - swifter >=1.3.4 + - pyarrow >=11.0.0 + - dill >=0.3.6 + - pytables >=3.8.0 + - markupsafe >=2.0.1 + - mmseqs2 >=15.6f452 + - bioinfokit >=2.1.3 + +test: + commands: + - vcontact3 --help + +about: + home: https://bitbucket.org/MAVERICLab/vcontact3 + license: GPLv3 + license_file: LICENSE + license_family: GPL + summary: Viral Contig Automatic Clustering and Taxonomy + doc_url: https://bitbucket.org/MAVERICLab/vcontact3/src/master/README.md \ No newline at end of file From 82075dae1e86fdc6aada9521a19dfba431255679 Mon Sep 17 00:00:00 2001 From: Katy Brown Date: Fri, 10 May 2024 04:14:36 +0100 Subject: [PATCH 65/81] Update meta.yaml (#47635) added missing dependency - scipy --- recipes/cialign/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/cialign/meta.yaml b/recipes/cialign/meta.yaml index e3e5b5b43dfbe6..a77d41ba8606b6 100644 --- a/recipes/cialign/meta.yaml +++ b/recipes/cialign/meta.yaml @@ -10,7 +10,7 @@ source: sha256: 8244cd7402ce7a9eea2bec2ca7954ef58b01408537c962611e60d7eb97a43966 build: - number: 1 + number: 2 script: "{{ PYTHON }} -m pip install . -vv" noarch: python run_exports: @@ -23,12 +23,14 @@ requirements: - numpy - pillow - pandas + - scipy - pip - python >=3.6 run: - configargparse - matplotlib-base - numpy + - scipy - pillow - pandas - python >=3.6 From 70b58a1cf661055ea3faa330be69e5938c2c34c9 Mon Sep 17 00:00:00 2001 From: Natasha Pavlovikj Date: Thu, 9 May 2024 23:03:58 -0500 Subject: [PATCH 66/81] Update libcifpp version (#47810) * Update libcifpp version * Fix url * Skip cron script * Fix typo --------- Co-authored-by: Natasha Pavlovikj --- recipes/libcifpp/build.sh | 8 +++--- recipes/libcifpp/conda_build_config.yaml | 7 ----- recipes/libcifpp/meta.yaml | 34 ++++++++++++++---------- 3 files changed, 25 insertions(+), 24 deletions(-) delete mode 100644 recipes/libcifpp/conda_build_config.yaml diff --git a/recipes/libcifpp/build.sh b/recipes/libcifpp/build.sh index b8317b473a8117..fd0933e91291dc 100644 --- a/recipes/libcifpp/build.sh +++ b/recipes/libcifpp/build.sh @@ -1,6 +1,8 @@ +#!/bin/bash + mkdir build cd build -cmake .. -DCMAKE_INSTALL_PREFIX=$PREFIX + +cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_TESTING=OFF -DCIFPP_DOWNLOAD_CCD=OFF -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCIFPP_INSTALL_UPDATE_SCRIPT=OFF .. cmake --build . --config Release -ctest -C Release -cmake --install . --prefix $PREFIX +cmake --install . --prefix ${PREFIX} diff --git a/recipes/libcifpp/conda_build_config.yaml b/recipes/libcifpp/conda_build_config.yaml deleted file mode 100644 index 1271f9dfbd2951..00000000000000 --- a/recipes/libcifpp/conda_build_config.yaml +++ /dev/null @@ -1,7 +0,0 @@ -# current version does not build with newer compilers -cxx_compiler_version: - - 10 # [linux] - - 14 # [osx] -c_compiler_version: - - 10 # [linux] - - 14 # [osx] diff --git a/recipes/libcifpp/meta.yaml b/recipes/libcifpp/meta.yaml index 59df774ff30987..b96240ab6abfdd 100644 --- a/recipes/libcifpp/meta.yaml +++ b/recipes/libcifpp/meta.yaml @@ -1,41 +1,47 @@ -{% set version = "5.0.0" %} +{% set name = "libcifpp" %} +{% set version = "7.0.3" %} +{% set sha256 = "c9d0ebe558dc5c5cebe212550c64b5d1f0671b374523865fbbda2beaa98beacc" %} package: - name: libcifpp + name: {{ name|lower }} version: {{ version }} source: - git_url: https://github.com/PDB-REDO/libcifpp - git_tag: "v{{ version }}" - sha256: fc1ed30d9bddddc10f32f96bb7fc9cb82430c93d012a7cd17d69678287542dec - -test: - commands: - - test -e $PREFIX/lib/libcifpp.a + url: https://github.com/PDB-REDO/{{ name|lower }}/archive/v{{ version }}.tar.gz + sha256: {{ sha256 }} build: skip: True # [osx] - number: 2 + number: 0 run_exports: - - {{ pin_subpackage('libcifpp', max_pin='x.x') }} + - {{ pin_subpackage(name|lower, max_pin="x") }} requirements: build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - boost-cpp - cmake - make + host: + - zlib + - boost-cpp + run: + - zlib + - boost-cpp +test: + commands: + - test -e $PREFIX/lib/libcifpp.a + about: home: https://github.com/PDB-REDO/libcifpp license: BSD-2-Clause license_file: LICENSE license_family: BSD summary: Library containing code to manipulate mmCIF and PDB files + doc_url: https://pdb-redo.github.io/libcifpp/ + dev_url: https://github.com/PDB-REDO/libcifpp extra: recipe-maintainers: - multimeric - skip-lints: - - uses_vcs_url From 139a041aacc499ff333e47de71fac96a1b0ef9cb Mon Sep 17 00:00:00 2001 From: wjunLu <135617475+wjunLu@users.noreply.github.com> Date: Fri, 10 May 2024 12:13:09 +0800 Subject: [PATCH 67/81] Add aarch64 build for wise2 (#47579) * Test * Fix bug * Fix bug * Fix bug * Fix bug --- recipes/wise2/meta.yaml | 10 ++++++++-- recipes/wise2/patch | 26 ++++++++++++++++++++++++++ 2 files changed, 34 insertions(+), 2 deletions(-) diff --git a/recipes/wise2/meta.yaml b/recipes/wise2/meta.yaml index cdc27595f5017f..0852d41a13f5bd 100644 --- a/recipes/wise2/meta.yaml +++ b/recipes/wise2/meta.yaml @@ -5,13 +5,15 @@ package: version: '{{ version }}' source: - url: https://www.ebi.ac.uk/~birney/wise2/wise{{ version }}.tar.gz + url: https://www.ebi.ac.uk/~birney/wise{{ version }}.tar.gz sha256: 240e2b12d6cd899040e2efbcb85b0d3c10245c255f3d07c1db45d0af5a4d5fa1 patches: - patch build: - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("wise2", max_pin='x.x') }} requirements: build: @@ -32,3 +34,7 @@ about: home: https://www.ebi.ac.uk/~birney/wise2/ license: Public Domain summary: The Wise2.4 package is the "revival" release of Wise2 + +extra: + additional-platforms: + - linux-aarch64 diff --git a/recipes/wise2/patch b/recipes/wise2/patch index 02df512f427062..8a63165a5c0932 100644 --- a/recipes/wise2/patch +++ b/recipes/wise2/patch @@ -23,3 +23,29 @@ index 7fd404a..4fbb930 100644 # These are the CFLAGS to use. These days Wise2 is inherently # pthreaded, and everything is compiled with threads. However +diff --git a/src/dnaindex/compressed_protein_index.c b/src/dnaindex/compressed_protein_index.c +index 00720b5..85227d0 100644 +--- a/src/dnaindex/compressed_protein_index.c ++++ b/src/dnaindex/compressed_protein_index.c +@@ -199,7 +199,7 @@ boolean add_direct_number_CompressedProteinIndex(void * data,int seq_number,Sequ + { + fatal("For compressed protein indexes, impossible to add numbers directly"); + +- return NULL; ++ return FALSE; + } + + # line 226 "compressed_protein_index.dy" +diff --git a/src/models/motifmatrix.c b/src/models/motifmatrix.c +index 8c6a8aa..bfb2270 100644 +--- a/src/models/motifmatrix.c ++++ b/src/models/motifmatrix.c +@@ -407,7 +407,7 @@ MotifConsMatrix * MotifConsMatrix_alloc_matrix(int leni,int lenj) + + for(i=0;imat[i][j] = NULL; ++ out->mat[i][j] = '0'; + } + + \ No newline at end of file From c90822fbf6918f641c4787e69d2a328a2f7e9821 Mon Sep 17 00:00:00 2001 From: wjunLu <135617475+wjunLu@users.noreply.github.com> Date: Fri, 10 May 2024 12:24:05 +0800 Subject: [PATCH 68/81] Add aarch64 build for necat (#47733) * Merge all commits * clean up recipe --------- Co-authored-by: mencian --- recipes/necat/build.sh | 19 ++++++++----- recipes/necat/meta.yaml | 28 ++++++++++++++----- recipes/necat/src_ctg_cns_filter_m4.mk.patch | 13 +++++++++ ...mk.patch => src_ctg_cns_pm4_main.mk.patch} | 6 ++-- .../src_partition_candidates_main.mk.patch | 2 +- recipes/necat/src_partition_m4_main.mk.patch | 2 +- .../src_trim_bases_accurate0_pm4.mk.patch | 2 +- .../src_trim_bases_accurate_pm4.mk.patch | 12 ++++---- ...trim_bases_extract_trimmerd_reads.mk.patch | 2 +- ...rc_trim_bases_largest_cover_range.mk.patch | 2 +- recipes/necat/src_trim_bases_pm4.mk.patch | 2 +- 11 files changed, 61 insertions(+), 29 deletions(-) create mode 100644 recipes/necat/src_ctg_cns_filter_m4.mk.patch rename recipes/necat/{src_pm4_main.mk.patch => src_ctg_cns_pm4_main.mk.patch} (73%) diff --git a/recipes/necat/build.sh b/recipes/necat/build.sh index 7b6ab162326f03..8d430300b1ee67 100644 --- a/recipes/necat/build.sh +++ b/recipes/necat/build.sh @@ -1,23 +1,28 @@ #!/bin/bash set -ex -export CFLAGS="$CFLAGS -I$PREFIX/include" -export CXXFLAGS="$CXXFLAGS -I$PREFIX/include" -export LDFLAGS="$LDFLAGS -L$PREFIX/lib" +export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" +export CFLAGS="${CFLAGS} -O3 -I${PREFIX}/include" +export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" + +BIN_ROOT="Linux-amd64/bin" +case $(uname -m) in + arm64|aarch64) BIN_ROOT="Linux-aarch64/bin" ;; +esac # build -make -C src CFLAGS+="${CFLAGS}" LDFLAGS+="${LDFLAGS}" CXXFLAGS+="${CXXFLAGS}" +make -C src CFLAGS+="${CFLAGS}" LDFLAGS+="${LDFLAGS}" CXXFLAGS+="${CXXFLAGS}" -j"${CPU_COUNT}" # create and populate binary file mkdir -p $PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin/ -cp -r Linux-amd64/bin/* $PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin/ +cp -rf $BIN_ROOT/* $PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin/ # create calling script -mkdir $PREFIX/bin/ +mkdir -p ${PREFIX}/bin/ cat < $PREFIX/bin/necat #!/bin/bash PATH=\$PATH:$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM/bin/ necat.pl "\$@" EOF -chmod +x $PREFIX/bin/necat +chmod 755 ${PREFIX}/bin/necat diff --git a/recipes/necat/meta.yaml b/recipes/necat/meta.yaml index 5b659eee694750..662576b73a10ff 100644 --- a/recipes/necat/meta.yaml +++ b/recipes/necat/meta.yaml @@ -1,8 +1,9 @@ +{% set name = "necat" %} {% set version = "0.0.1_update20200803" %} {% set sha256 = "5ddd147b5be6b1fac2f6c10b18c9b587838f2304d2584087c4ed6f628eced06c" %} package: - name: necat + name: {{ name }} version: {{ version }} source: @@ -36,10 +37,11 @@ source: - src_renumber_sequences_main.mk.patch - src_reorder_cns_reads_main.mk.patch - src_ctg_cns_main.mk.patch + - src_ctg_cns_filter_m4.mk.patch + - src_ctg_cns_pm4_main.mk.patch - src_ctgpm_ctgpm.mk.patch - src_ctgpm_fix_can_info.mk.patch - src_ctgpm_split_ctgs.mk.patch - - src_pm4_main.mk.patch - src_preprocess_raw_reads_main.mk.patch - src_reference_mapping_rm_one_vol_main.mk.patch - src_fsa_fsa.mk.patch @@ -52,7 +54,9 @@ source: build: skip: True # [osx] - number: 4 + number: 5 + run_exports: + - {{ pin_subpackage("necat", max_pin="x.x") }} requirements: build: @@ -67,9 +71,19 @@ requirements: test: commands: - - necat | grep Usage + - necat | grep "Usage" about: - home: https://github.com/xiaochuanle/NECAT - license: Unknow - summary: Nanopore data assembler + home: "https://github.com/xiaochuanle/NECAT" + license: Unknown + summary: "NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads." + dev_url: "https://github.com/xiaochuanle/NECAT" + doc_url: "https://github.com/xiaochuanle/NECAT/blob/master/README.md" + +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - doi:10.1038/s41467-020-20236-7 + - biotools:necat + - usegalaxy-eu:necat diff --git a/recipes/necat/src_ctg_cns_filter_m4.mk.patch b/recipes/necat/src_ctg_cns_filter_m4.mk.patch new file mode 100644 index 00000000000000..2ab69d0e972978 --- /dev/null +++ b/recipes/necat/src_ctg_cns_filter_m4.mk.patch @@ -0,0 +1,13 @@ +diff --git a/src/ctg_cns/filter_m4.mk b/src/ctg_cns/filter_m4.mk +index 822129e..77b441c 100644 +--- a/src/ctg_cns/filter_m4.mk ++++ b/src/ctg_cns/filter_m4.mk +@@ -11,7 +11,7 @@ SOURCES := filter_m4.c pm4.c load_ctg_read_ids.c + SRC_INCDIRS := . + + TGT_LDFLAGS := -L${TARGET_DIR} +-TGT_LDLIBS := -lontcns ++TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++ -lm + TGT_PREREQS := libontcns.a + + SUBMAKEFILES := \ No newline at end of file diff --git a/recipes/necat/src_pm4_main.mk.patch b/recipes/necat/src_ctg_cns_pm4_main.mk.patch similarity index 73% rename from recipes/necat/src_pm4_main.mk.patch rename to recipes/necat/src_ctg_cns_pm4_main.mk.patch index 092aca420585dd..49e7239b93bc8f 100644 --- a/recipes/necat/src_pm4_main.mk.patch +++ b/recipes/necat/src_ctg_cns_pm4_main.mk.patch @@ -1,5 +1,5 @@ diff --git a/src/ctg_cns/pm4_main.mk b/src/ctg_cns/pm4_main.mk -index a020fb3..04c17c5 100644 +index a020fb3..a536385 100644 --- a/src/ctg_cns/pm4_main.mk +++ b/src/ctg_cns/pm4_main.mk @@ -11,7 +11,7 @@ SOURCES := pm4_main.c pm4.c @@ -7,7 +7,7 @@ index a020fb3..04c17c5 100644 TGT_LDFLAGS := -L${TARGET_DIR} -TGT_LDLIBS := -lontcns -+TGT_LDLIBS := -lontcns -lpthread ++TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++ -lm TGT_PREREQS := libontcns.a - SUBMAKEFILES := + SUBMAKEFILES := \ No newline at end of file diff --git a/recipes/necat/src_partition_candidates_main.mk.patch b/recipes/necat/src_partition_candidates_main.mk.patch index 87da273e6066d7..56f01b1d0b53f5 100644 --- a/recipes/necat/src_partition_candidates_main.mk.patch +++ b/recipes/necat/src_partition_candidates_main.mk.patch @@ -7,7 +7,7 @@ index 19c70f0..0581c1f 100644 TGT_LDFLAGS := -L${TARGET_DIR} -TGT_LDLIBS := -lontcns -+TGT_LDLIBS := -lontcns -lpthread ++TGT_LDLIBS := -lontcns -lz -lpthread TGT_PREREQS := libontcns.a SUBMAKEFILES := diff --git a/recipes/necat/src_partition_m4_main.mk.patch b/recipes/necat/src_partition_m4_main.mk.patch index 8487acf4dcacc6..01ad339e7b650e 100644 --- a/recipes/necat/src_partition_m4_main.mk.patch +++ b/recipes/necat/src_partition_m4_main.mk.patch @@ -7,7 +7,7 @@ index 6265052..805ff27 100644 TGT_LDFLAGS := -L${TARGET_DIR} -TGT_LDLIBS := -lontcns -+TGT_LDLIBS := -lontcns -lpthread ++TGT_LDLIBS := -lontcns lz -lpthread TGT_PREREQS := libontcns.a SUBMAKEFILES := diff --git a/recipes/necat/src_trim_bases_accurate0_pm4.mk.patch b/recipes/necat/src_trim_bases_accurate0_pm4.mk.patch index 58408c947c58e4..a17935c78e2bf1 100644 --- a/recipes/necat/src_trim_bases_accurate0_pm4.mk.patch +++ b/recipes/necat/src_trim_bases_accurate0_pm4.mk.patch @@ -7,7 +7,7 @@ index df2e71b..b56e887 100644 TGT_LDFLAGS := -L${TARGET_DIR} -TGT_LDLIBS := -lontcns -+TGT_LDLIBS := -lontcns -lpthread ++TGT_LDLIBS := -lontcns -lz -lpthread TGT_PREREQS := libontcns.a SUBMAKEFILES := diff --git a/recipes/necat/src_trim_bases_accurate_pm4.mk.patch b/recipes/necat/src_trim_bases_accurate_pm4.mk.patch index 986b05ccbfe4a4..ad77bb55caa15d 100644 --- a/recipes/necat/src_trim_bases_accurate_pm4.mk.patch +++ b/recipes/necat/src_trim_bases_accurate_pm4.mk.patch @@ -1,13 +1,13 @@ -diff --git a/src/trim_bases_accurate/pm4.mk b/src/trim_bases_accurate/pm4.mk -index 0d9d277..dcba7cf 100644 ---- a/src/trim_bases_accurate/pm4.mk -+++ b/src/trim_bases_accurate/pm4.mk -@@ -11,7 +11,7 @@ SOURCES := pm4_aux.c pm4_main.c +diff --git a/src/trim_bases_accurate/pm4.mk b/src/trim_bases_accurate/pm4.mk +index 0d9d277..dcba7cf 100644 +--- a/src/trim_bases_accurate/pm4.mk ++++ b/src/trim_bases_accurate/pm4.mk +@@ -11,7 +11,7 @@ SOURCES := pm4_aux.c pm4_main.c SRC_INCDIRS := . TGT_LDFLAGS := -L${TARGET_DIR} -TGT_LDLIBS := -lontcns -+TGT_LDLIBS := -lontcns -lpthread ++TGT_LDLIBS := -lontcns -lz -lpthread TGT_PREREQS := libontcns.a SUBMAKEFILES := diff --git a/recipes/necat/src_trim_bases_extract_trimmerd_reads.mk.patch b/recipes/necat/src_trim_bases_extract_trimmerd_reads.mk.patch index af03197a3a694f..9068fa5a2e0e14 100644 --- a/recipes/necat/src_trim_bases_extract_trimmerd_reads.mk.patch +++ b/recipes/necat/src_trim_bases_extract_trimmerd_reads.mk.patch @@ -6,7 +6,7 @@ index 8f493f1..4d06513 100644 SRC_INCDIRS := . -+TGT_LDLIBS := -lontcns -lz -lpthread ++TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++ -lm TGT_LDFLAGS := -L${TARGET_DIR} -TGT_LDLIBS := -lontcns TGT_PREREQS := libontcns.a diff --git a/recipes/necat/src_trim_bases_largest_cover_range.mk.patch b/recipes/necat/src_trim_bases_largest_cover_range.mk.patch index 04f183ebd8b881..f119a87a2cbd2d 100644 --- a/recipes/necat/src_trim_bases_largest_cover_range.mk.patch +++ b/recipes/necat/src_trim_bases_largest_cover_range.mk.patch @@ -7,7 +7,7 @@ index 17134bf..9e89659 100644 TGT_LDFLAGS := -L${TARGET_DIR} -TGT_LDLIBS := -lontcns -+TGT_LDLIBS := -lontcns -lpthread ++TGT_LDLIBS := -lontcns -lz -lpthread -lstdc++ -lm TGT_PREREQS := libontcns.a SUBMAKEFILES := diff --git a/recipes/necat/src_trim_bases_pm4.mk.patch b/recipes/necat/src_trim_bases_pm4.mk.patch index e7746d1e8a2119..7ce20fdc1583c9 100644 --- a/recipes/necat/src_trim_bases_pm4.mk.patch +++ b/recipes/necat/src_trim_bases_pm4.mk.patch @@ -7,7 +7,7 @@ index d007c96..778a4d2 100644 TGT_LDFLAGS := -L${TARGET_DIR} -TGT_LDLIBS := -lontcns -+TGT_LDLIBS := -lontcns -lpthread ++TGT_LDLIBS := -lontcns -lz -lpthread TGT_PREREQS := libontcns.a SUBMAKEFILES := From ced3555b1a53ee1b435a2dbb6a874c9edb89ead5 Mon Sep 17 00:00:00 2001 From: CG Group <127956711+LuoGroup2023@users.noreply.github.com> Date: Fri, 10 May 2024 13:15:58 +0800 Subject: [PATCH 69/81] add dechat (#47794) * add dechat * clean up recipe --------- Co-authored-by: yichenli <923781272@qq.com> Co-authored-by: mencian --- recipes/dechat/build.sh | 13 ++++++++++++ recipes/dechat/meta.yaml | 44 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) create mode 100644 recipes/dechat/build.sh create mode 100644 recipes/dechat/meta.yaml diff --git a/recipes/dechat/build.sh b/recipes/dechat/build.sh new file mode 100644 index 00000000000000..afa7523a8daa57 --- /dev/null +++ b/recipes/dechat/build.sh @@ -0,0 +1,13 @@ +#!/usr/bin/env bash + +mkdir -p ${PREFIX}/bin + +if [ "$(uname)" == "Darwin" ]; then + cp -f ${SRC_DIR}/bin/dechat ${PREFIX}/bin/ +else + mkdir build && cd build + cmake -DCMAKE_INSTALL_PREFIX:PATH="${PREFIX}" -DKSIZE_LIST="32 64 96 128 160 192" .. + make -j"${CPU_COUNT}" + chmod 755 ${SRC_DIR}/bin/dechat + cp -f ${SRC_DIR}/bin/dechat ${PREFIX}/bin/ +fi diff --git a/recipes/dechat/meta.yaml b/recipes/dechat/meta.yaml new file mode 100644 index 00000000000000..190e22d63e07ba --- /dev/null +++ b/recipes/dechat/meta.yaml @@ -0,0 +1,44 @@ +{% set name = "dechat" %} +{% set version = "1.0.0" %} + +package: + name: {{ name }} + version: {{ version }} + +source: + url: https://github.com/LuoGroup2023/DeChat/releases/download/v{{ version }}/{{ name }}.tar.gz + sha256: 68469147b5386272a6a419eaa7fa7bafb4ddfe03a7ee57da795764b0b31f3845 + +build: + number: 0 + run_exports: + - {{ pin_subpackage('dechat', max_pin="x") }} + +requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make + - cmake + host: + - zlib + - boost-cpp ==1.67.0 + - sparsehash + - pkg-config + - libdivsufsort + - hdf5 + run: + - boost-cpp ==1.67.0 # [osx] + - libdivsufsort # [osx] + - hdf5 + +test: + commands: + - (dechat -h || true) + +about: + home: "https://github.com/LuoGroup2023/DeChat" + license: MIT + license_family: MIT + summary: Repeat and haplotype aware error correction in nanopore sequencing reads with Dechat + dev_url: "https://github.com/LuoGroup2023/DeChat" From a1bce9f32e67433cd6f1ef07a7807a0d602ff0f7 Mon Sep 17 00:00:00 2001 From: Shuai WANG <48624090+wshuai294@users.noreply.github.com> Date: Fri, 10 May 2024 20:24:02 +0800 Subject: [PATCH 70/81] add pstrain (#47552) * add pstrain * pstrain2 * pstrain3 * pstrain4 * pstrain5 * pstrain6 * generic * generic2 * no generic * support metaphlan4 * update source code * Update recipes/pstrain/build.sh Co-authored-by: Martin Grigorov * Update recipes/pstrain/build.sh Co-authored-by: Martin Grigorov * Update recipes/pstrain/build.sh Co-authored-by: Martin Grigorov * generic * generic * generic * generic --------- Co-authored-by: Martin Grigorov --- recipes/pstrain/build.sh | 8 +++++++ recipes/pstrain/meta.yaml | 48 +++++++++++++++++++++++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 recipes/pstrain/build.sh create mode 100644 recipes/pstrain/meta.yaml diff --git a/recipes/pstrain/build.sh b/recipes/pstrain/build.sh new file mode 100644 index 00000000000000..792771b573bf46 --- /dev/null +++ b/recipes/pstrain/build.sh @@ -0,0 +1,8 @@ +#!/bin/bash + +mkdir -p $PREFIX/bin + +cp $SRC_DIR/scripts/*.py $PREFIX/bin +cp $SRC_DIR/scripts/*.sh $PREFIX/bin +cp $SRC_DIR/scripts/*.jar $PREFIX/bin + diff --git a/recipes/pstrain/meta.yaml b/recipes/pstrain/meta.yaml new file mode 100644 index 00000000000000..039b168857727d --- /dev/null +++ b/recipes/pstrain/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.3" %} + +package: + name: pstrain + version: {{ version }} + +build: + number: 0 + run_exports: + - {{ pin_subpackage("pstrain", max_pin="x") }} + entry_points: + - pstrain = PStrain:main + +source: + url: https://github.com/wshuai294/PStrain/archive/refs/tags/v{{ version }}.tar.gz + sha256: a78315a87048335045d0e1ec3123f33f75327d627a03b17aaa003990d2375214 + +requirements: + build: +# noarch: generic + host: + run: + - python >=3.7 + - metaphlan ==4 + - pysam + - numpy + - pulp + - samtools + - bowtie2 + - openjdk + + +about: + home: https://github.com/wshuai294/PStrain + license: MIT + summary: An Iterative Microbial Strains Profiling Algorithm for Shotgun Metagenomic Sequencing Data + +test: + commands: + - pstrain --help + +extra: + skip-lints: + - should_be_noarch_generic + identifiers: + - biotools:pstrain + recipe-maintainers: + - wshuai294 From 4e6ca6759e51bfe1cdf86e13d405bd58ac9cd201 Mon Sep 17 00:00:00 2001 From: Jeremy Volkening Date: Fri, 10 May 2024 07:51:23 -0500 Subject: [PATCH 71/81] remove perl-compress-bgzf (moved to conda-forge) (#45380) --- recipes/perl-compress-bgzf/0.005/build.sh | 21 ------------ recipes/perl-compress-bgzf/0.005/meta.yaml | 37 ---------------------- 2 files changed, 58 deletions(-) delete mode 100644 recipes/perl-compress-bgzf/0.005/build.sh delete mode 100644 recipes/perl-compress-bgzf/0.005/meta.yaml diff --git a/recipes/perl-compress-bgzf/0.005/build.sh b/recipes/perl-compress-bgzf/0.005/build.sh deleted file mode 100644 index 34660971a24c85..00000000000000 --- a/recipes/perl-compress-bgzf/0.005/build.sh +++ /dev/null @@ -1,21 +0,0 @@ -#!/bin/bash - -# If it has Build.PL use that, otherwise use Makefile.PL -if [ -f Build.PL ]; then - perl Build.PL - perl ./Build - perl ./Build test - # Make sure this goes in site - perl ./Build install --installdirs site -elif [ -f Makefile.PL ]; then - # Make sure this goes in site - perl Makefile.PL INSTALLDIRS=site - make - make test - make install -else - echo 'Unable to find Build.PL or Makefile.PL. You need to modify build.sh.' - exit 1 -fi -# Workaround https://github.com/conda/conda-build/issues/2824 -chmod u+w $PREFIX/bin/bgzip.pl diff --git a/recipes/perl-compress-bgzf/0.005/meta.yaml b/recipes/perl-compress-bgzf/0.005/meta.yaml deleted file mode 100644 index f1cc877c3f17fe..00000000000000 --- a/recipes/perl-compress-bgzf/0.005/meta.yaml +++ /dev/null @@ -1,37 +0,0 @@ -{% set name = "perl-compress-bgzf" %} -{% set version = "0.005" %} -{% set sha256 = "1b40284f2ca965ee20ea91707c41005f978127a9bf358a233f637b286adf1f3f" %} - -package: - name: {{ name }} - version: {{ version }} - -source: - url: https://cpan.metacpan.org/authors/id/V/VO/VOLKENING/Compress-BGZF-0.005.tar.gz - sha256: {{ sha256 }} - -build: - noarch: generic - number: 1 - -requirements: - build: - - make - host: - - perl - - perl-extutils-makemaker - - perl-test-more - - run: - - perl - -test: - imports: - - Compress::BGZF - - Compress::BGZF::Reader - - Compress::BGZF::Writer - -about: - home: http://metacpan.org/pod/Compress::BGZF - license: gpl_3 - summary: 'Read/write blocked GZIP (BGZF) files' From 8c851c71e435fd48517bd13a15e248e7bd257945 Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 10 May 2024 17:27:03 +0300 Subject: [PATCH 72/81] Add Linux aarch64 build for more Bioconductor packages (#47788) * Add Linux aarch64 build for more Bioconductor packages - flowfp - flowsom - genenetworkbuilder - maigespack - metaseq - mnem - monocle - msnbase - netresponse Signed-off-by: Martin Tzvetanov Grigorov * Update the pins for maigespack's bioconductor dependencies Signed-off-by: Martin Tzvetanov Grigorov * Add linux-aarch64 builds for bioconductor-vsn and r-leidenbase Signed-off-by: Martin Tzvetanov Grigorov * Update r-leidenbase to 0.1.27 Signed-off-by: Martin Tzvetanov Grigorov * Undo bioc-flowfp, -metaseq and -monocle for this PR The build does not pass in 1 hour CircleCI They will be done in a separate PR Signed-off-by: Martin Tzvetanov Grigorov * Revert r-leidenbase changes. They will be part of #47800 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bioconductor-flowsom/meta.yaml | 6 +++-- .../bioconductor-genenetworkbuilder/meta.yaml | 9 ++++++-- recipes/bioconductor-maigespack/meta.yaml | 22 ++++++++++--------- recipes/bioconductor-mnem/meta.yaml | 9 ++++++-- recipes/bioconductor-msnbase/meta.yaml | 4 +++- recipes/bioconductor-netresponse/meta.yaml | 10 +++++++-- 6 files changed, 41 insertions(+), 19 deletions(-) diff --git a/recipes/bioconductor-flowsom/meta.yaml b/recipes/bioconductor-flowsom/meta.yaml index e8708a748755e8..b149ec1e272b14 100644 --- a/recipes/bioconductor-flowsom/meta.yaml +++ b/recipes/bioconductor-flowsom/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 9bc309cc9948473d101d91ba6f1a37f2 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -64,11 +64,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'GPL-3.0-or-later' summary: 'Using self-organizing maps for visualization and interpretation of cytometry data' description: 'FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:flowsom - doi:10.1002/cyto.a.22625 diff --git a/recipes/bioconductor-genenetworkbuilder/meta.yaml b/recipes/bioconductor-genenetworkbuilder/meta.yaml index 40e22076b24fda..840e50663cdde6 100644 --- a/recipes/bioconductor-genenetworkbuilder/meta.yaml +++ b/recipes/bioconductor-genenetworkbuilder/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: aedb0b143d59865acfad5ce4d635ff77 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -49,8 +49,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'GPL-3.0-or-later' summary: 'GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data' description: 'Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-maigespack/meta.yaml b/recipes/bioconductor-maigespack/meta.yaml index fdd8923643d43c..035f65069b988d 100644 --- a/recipes/bioconductor-maigespack/meta.yaml +++ b/recipes/bioconductor-maigespack/meta.yaml @@ -13,25 +13,25 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 118a586912fcef7e97526e4b2d142729 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ # Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som requirements: host: - - 'bioconductor-convert >=1.76.0,<1.77.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-convert >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.1,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base - libblas - liblapack run: - - 'bioconductor-convert >=1.76.0,<1.77.0' - - 'bioconductor-graph >=1.78.0,<1.79.0' - - 'bioconductor-limma >=3.56.0,<3.57.0' - - 'bioconductor-marray >=1.78.0,<1.79.0' + - 'bioconductor-convert >=1.78.0,<1.79.0' + - 'bioconductor-graph >=1.80.0,<1.81.0' + - 'bioconductor-limma >=3.58.1,<3.59.0' + - 'bioconductor-marray >=1.80.0,<1.81.0' - r-base build: - {{ compiler('c') }} @@ -41,11 +41,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' + license: 'GPL-3.0-or-later' summary: 'Functions to handle cDNA microarray data, including several methods of data analysis' description: 'This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:maigespack - doi:10.1038/nmeth.3252 diff --git a/recipes/bioconductor-mnem/meta.yaml b/recipes/bioconductor-mnem/meta.yaml index 10fae6b84f0a82..ecf09bdc621429 100644 --- a/recipes/bioconductor-mnem/meta.yaml +++ b/recipes/bioconductor-mnem/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 630cb52a48148dc82038613aacb4e834 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -67,8 +67,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3.0-only summary: 'Mixture Nested Effects Models' description: 'Mixture Nested Effects Models (mnem) is an extension of Nested Effects Models and allows for the analysis of single cell perturbation data provided by methods like Perturb-Seq (Dixit et al., 2016) or Crop-Seq (Datlinger et al., 2017). In those experiments each of many cells is perturbed by a knock-down of a specific gene, i.e. several cells are perturbed by a knock-down of gene A, several by a knock-down of gene B, ... and so forth. The observed read-out has to be multi-trait and in the case of the Perturb-/Crop-Seq gene are expression profiles for each cell. mnem uses a mixture model to simultaneously cluster the cell population into k clusters and and infer k networks causally linking the perturbed genes for each cluster. The mixture components are inferred via an expectation maximization algorithm.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} diff --git a/recipes/bioconductor-msnbase/meta.yaml b/recipes/bioconductor-msnbase/meta.yaml index a3dd29afe1be05..9ee30e970c999e 100644 --- a/recipes/bioconductor-msnbase/meta.yaml +++ b/recipes/bioconductor-msnbase/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 4d3cbd696e9ca193ec9bdc4722f2ac49 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -83,6 +83,8 @@ about: summary: 'Base Functions and Classes for Mass Spectrometry and Proteomics' description: 'MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:msnbase parent_recipe: diff --git a/recipes/bioconductor-netresponse/meta.yaml b/recipes/bioconductor-netresponse/meta.yaml index c0beb901e67b00..8f03e8e1a4efde 100644 --- a/recipes/bioconductor-netresponse/meta.yaml +++ b/recipes/bioconductor-netresponse/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 990c864cea311427d5af5f854edf4041 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -58,8 +58,14 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>=2)' + license: 'GPL-3.0-or-later' summary: 'Functional Network Analysis' description: 'Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' +extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} + From 3b5075ee9e52df20239bc822073488af69b34a9c Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 10 May 2024 17:27:53 +0300 Subject: [PATCH 73/81] Add Linux aarch64 build for more Bioconductor packages (#47800) * Add Linux aarch64 build for more Bioconductor packages - flowfp - metaseq - monocle Signed-off-by: Martin Tzvetanov Grigorov * Build r-leidenbase for linux-aarch64 Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bioconductor-flowfp/meta.yaml | 4 +++- recipes/bioconductor-metaseq/meta.yaml | 4 +++- recipes/bioconductor-monocle/meta.yaml | 4 +++- recipes/r-leidenbase/meta.yaml | 12 ++++++++---- 4 files changed, 17 insertions(+), 7 deletions(-) diff --git a/recipes/bioconductor-flowfp/meta.yaml b/recipes/bioconductor-flowfp/meta.yaml index 680a77375956ca..8d91ab91bc4af7 100644 --- a/recipes/bioconductor-flowfp/meta.yaml +++ b/recipes/bioconductor-flowfp/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 5f0424d8a662d2d65bacbcff080d9c7a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -47,6 +47,8 @@ about: summary: 'Fingerprinting for Flow Cytometry' description: 'Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:flowfp - doi:10.1155/2009/193947 diff --git a/recipes/bioconductor-metaseq/meta.yaml b/recipes/bioconductor-metaseq/meta.yaml index 564aeea18d8a0a..8aafac7b3bdf8d 100644 --- a/recipes/bioconductor-metaseq/meta.yaml +++ b/recipes/bioconductor-metaseq/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 8c3ee60501395cc86ecda6817d0d5439 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -43,6 +43,8 @@ about: summary: 'Meta-analysis of RNA-Seq count data in multiple studies' description: 'The probabilities by one-sided NOISeq are combined by Fisher''s method or Stouffer''s method' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:metaseq - doi:10.1038/nmeth.3252 diff --git a/recipes/bioconductor-monocle/meta.yaml b/recipes/bioconductor-monocle/meta.yaml index 1877a38efe4cfe..0d97d8b9d68ad6 100644 --- a/recipes/bioconductor-monocle/meta.yaml +++ b/recipes/bioconductor-monocle/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 8b3a3d5cd2698b4cef4396c388250658 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -99,6 +99,8 @@ about: summary: 'Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq' description: 'Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:monocle parent_recipe: diff --git a/recipes/r-leidenbase/meta.yaml b/recipes/r-leidenbase/meta.yaml index 0894c430ee0cff..fcd2ae951d2977 100644 --- a/recipes/r-leidenbase/meta.yaml +++ b/recipes/r-leidenbase/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.1.18" %} +{% set version = "0.1.27" %} package: name: r-leidenbase @@ -6,10 +6,10 @@ package: source: url: https://cran.rstudio.com/src/contrib/leidenbase_{{ version }}.tar.gz - sha256: b56fa823bce97c98e886896111041d50b12c1d1aad4ec01a829851a537d0dbfd + sha256: c3168a68828aacfcf78c6c39415b4771f084c5b5c3c9b2e226dcb8cf909d7b27 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -38,5 +38,9 @@ test: about: home: https://cole-trapnell-lab.github.io/leidenbase/ - license: GPL2, GPL3, BSD + license: GPL-2.0-only, GPL-3.0-only, BSD summary: An R to C interface that runs the Leiden community detection algorithm to find a basic partition + +extra: + additional-platforms: + - linux-aarch64 \ No newline at end of file From 420bee3543d7c88763cbd27c57c2188fda8eec7b Mon Sep 17 00:00:00 2001 From: Martin Grigorov Date: Fri, 10 May 2024 17:29:24 +0300 Subject: [PATCH 74/81] Add Linux aarch64 build for more Bioconductor packages (#47789) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * iAdd Linux aarch64 build for more Bioconductor packages - bamsignals - bcrank - bcseq - beachmat - chromdraw - hdf5array - rsamtools Signed-off-by: Martin Tzvetanov Grigorov * Add linux-aarch64 build for bioconductor-rhdf5 too Signed-off-by: Martin Tzvetanov Grigorov * Add `tapi` as a dependency for bioconductor-beachmat ``` (ERR) dyld[44564]: Library not loaded: '@rpath/libtapi.dylib'␛[0m 2024-05-09T12:56:36.5989360Z 12:56:34 ␛[32mBIOCONDA INFO␛[0m (ERR) Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/x86_64-apple-darwin13.4.0-ld'␛[0m 2024-05-09T12:56:36.5991920Z 12:56:34 ␛[32mBIOCONDA INFO␛[0m (ERR) Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/../lib/libtapi.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/../lib/libtapi.dylib' (no such file), '/usr/local/lib/libtapi.dylib' (no such file), '/usr/lib/libtapi.dylib' (no such file)␛[0m 2024-05-09T12:56:36.5995710Z 12:56:34 ␛[32mBIOCONDA INFO␛[0m (ERR) clang-15: error: unable to execute command: Abort trap: 6␛[0m ``` Signed-off-by: Martin Tzvetanov Grigorov * Do not build bioc-bcseq and bioc-rsamtools for now. The build on OSX fails Signed-off-by: Martin Tzvetanov Grigorov --------- Signed-off-by: Martin Tzvetanov Grigorov --- recipes/bioconductor-bamsignals/meta.yaml | 6 ++++-- recipes/bioconductor-bcrank/meta.yaml | 6 ++++-- recipes/bioconductor-beachmat/meta.yaml | 11 +++++++++-- recipes/bioconductor-chromdraw/meta.yaml | 6 ++++-- recipes/bioconductor-hdf5array/meta.yaml | 4 +++- recipes/bioconductor-rhdf5/meta.yaml | 4 +++- 6 files changed, 27 insertions(+), 10 deletions(-) diff --git a/recipes/bioconductor-bamsignals/meta.yaml b/recipes/bioconductor-bamsignals/meta.yaml index fe492377680454..aa4d6567aedc30 100644 --- a/recipes/bioconductor-bamsignals/meta.yaml +++ b/recipes/bioconductor-bamsignals/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: e7b42351aa9651bdf7d429a6377143f5 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -48,11 +48,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 + license: GPL-2.0-only summary: 'Extract read count signals from bam files' description: 'This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:bamsignals - doi:10.1038/nmeth.3252 diff --git a/recipes/bioconductor-bcrank/meta.yaml b/recipes/bioconductor-bcrank/meta.yaml index e76407cf7cf0a9..52d59782460fad 100644 --- a/recipes/bioconductor-bcrank/meta.yaml +++ b/recipes/bioconductor-bcrank/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 6c551ab389af456ab76449642c01881a build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -36,11 +36,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 + license: GPL-2.0-only summary: 'Predicting binding site consensus from ranked DNA sequences' description: 'Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:bcrank - doi:10.1093/nar/gkp381 diff --git a/recipes/bioconductor-beachmat/meta.yaml b/recipes/bioconductor-beachmat/meta.yaml index b7ae4f0aa33600..3f65c0a6c6a2fc 100644 --- a/recipes/bioconductor-beachmat/meta.yaml +++ b/recipes/bioconductor-beachmat/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: ec47172a09aba997192731b4a5f2f284 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -30,6 +30,7 @@ requirements: - r-rcpp - libblas - liblapack + - tapi # [osx] run: - 'bioconductor-biocgenerics >=0.48.0,<0.49.0' - 'bioconductor-delayedarray >=0.28.0,<0.29.0' @@ -37,6 +38,8 @@ requirements: - r-base - r-matrix - r-rcpp + - tapi + - tapi # [osx] build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -46,11 +49,15 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3.0-only summary: 'Compiling Bioconductor to Handle Each Matrix Type' description: 'Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 + identifiers: + - biotools:{{ name|lower }} parent_recipe: name: bioconductor-beachmat path: recipes/bioconductor-beachmat diff --git a/recipes/bioconductor-chromdraw/meta.yaml b/recipes/bioconductor-chromdraw/meta.yaml index e92f8c236b474d..8a7c74b6822e0b 100644 --- a/recipes/bioconductor-chromdraw/meta.yaml +++ b/recipes/bioconductor-chromdraw/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: a2cb0f03cdde9853f68662b1783a2edb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -39,11 +39,13 @@ test: - '$R -e "library(''{{ name }}'')"' about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-3 + license: GPL-3.0-only summary: 'chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.' description: 'ChromDraw is a R package for drawing the schemes of karyotype(s) in the linear and circular fashion. It is possible to visualized cytogenetic marsk on the chromosomes. This tool has own input data format. Input data can be imported from the GenomicRanges data structure. This package can visualized the data in the BED file format. Here is requirement on to the first nine fields of the BED format. Output files format are *.eps and *.svg.' license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:chromdraw parent_recipe: diff --git a/recipes/bioconductor-hdf5array/meta.yaml b/recipes/bioconductor-hdf5array/meta.yaml index 6f725cd98876b3..c3284e5d6eadfb 100644 --- a/recipes/bioconductor-hdf5array/meta.yaml +++ b/recipes/bioconductor-hdf5array/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: c59fcd283e0f9877f68457524b9d86bb build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -57,6 +57,8 @@ about: summary: 'HDF5 backend for DelayedArray objects' description: 'Implement the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:hdf5array - doi:10.1038/nmeth.3252 diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 7e644a64ce0385..a7b53b6eee8451 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -13,7 +13,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 947e662fe5f427ed0cc839e8049b431e build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ @@ -47,6 +47,8 @@ about: summary: 'R Interface to HDF5' description: 'This package provides an interface between HDF5 and R. HDF5''s main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.' extra: + additional-platforms: + - linux-aarch64 identifiers: - biotools:rhdf5 parent_recipe: From 852ae0e9e03812ee99beb3924d31fd4ca2aa6ba0 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 May 2024 10:30:23 -0400 Subject: [PATCH 75/81] Update libcifpp to 7.0.4 (#47814) --- recipes/libcifpp/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/libcifpp/meta.yaml b/recipes/libcifpp/meta.yaml index b96240ab6abfdd..9bf132407346b0 100644 --- a/recipes/libcifpp/meta.yaml +++ b/recipes/libcifpp/meta.yaml @@ -1,6 +1,6 @@ {% set name = "libcifpp" %} -{% set version = "7.0.3" %} -{% set sha256 = "c9d0ebe558dc5c5cebe212550c64b5d1f0671b374523865fbbda2beaa98beacc" %} +{% set version = "7.0.4" %} +{% set sha256 = "324eda2f6874df32671cd984c7249bfae025ca3fe1bfd875cbef35b046408b88" %} package: name: {{ name|lower }} From 4e3600cd2c5bfff6b05908fe38da772b5d5b74b4 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 May 2024 10:30:37 -0400 Subject: [PATCH 76/81] Update binchicken to 0.10.5 (#47815) --- recipes/binchicken/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/binchicken/meta.yaml b/recipes/binchicken/meta.yaml index 08e18db208ba62..7d3a3dc62433d4 100644 --- a/recipes/binchicken/meta.yaml +++ b/recipes/binchicken/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "0.10.4" %} +{% set version = "0.10.5" %} {% set name = "binchicken" %} -{% set sha256 = "0a48da6e24e8c0b0d6746914d80991b1662180fcd58b987ae0925326d0007382" %} +{% set sha256 = "687430f21caba05f654c6ebd26147c9130265de4cfc49d5233d0bcf9fcb07162" %} package: name: binchicken From f4c1c6af9aea4d7a53eca4f9535333ef028fc987 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 May 2024 10:30:49 -0400 Subject: [PATCH 77/81] Update pymzml to 2.5.10 (#47817) --- recipes/pymzml/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/pymzml/meta.yaml b/recipes/pymzml/meta.yaml index a50f7ac2305cbc..63e3f837a8fa5d 100644 --- a/recipes/pymzml/meta.yaml +++ b/recipes/pymzml/meta.yaml @@ -1,10 +1,10 @@ package: name: pymzml - version: "2.5.9" + version: "2.5.10" source: - url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.9.tar.gz - sha256: a064aa48bcab79510e564f4d3d93e3546cc2939ceaa89726206ca95c74fccda2 + url: https://github.com/pymzml/pymzML/archive/refs/tags/v2.5.10.tar.gz + sha256: 539b1a08645514e7020646c8887f1c42bef0c9105f30a58c56bd91830bd4c728 build: number: 0 From 84e554aa3ab2d0f54cefbb2d9f2b0d54b96a517c Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 May 2024 11:43:37 -0400 Subject: [PATCH 78/81] Update pathogen-profiler to 4.2.0 (#47820) * Update pathogen-profiler to 4.2.0 * update shasum --------- Co-authored-by: Jody Phelan --- recipes/pathogen-profiler/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/pathogen-profiler/meta.yaml b/recipes/pathogen-profiler/meta.yaml index 7f7282124371c8..fa717d8bd23884 100644 --- a/recipes/pathogen-profiler/meta.yaml +++ b/recipes/pathogen-profiler/meta.yaml @@ -1,6 +1,6 @@ {% set name = "pathogen-profiler" %} -{% set version = "4.1.0" %} -{% set sha256 = "ddf7570f46f11ea7dae48dbd2d66811f4ed9c8d1b80a3e62049369ed01f22024" %} +{% set version = "4.2.0" %} +{% set sha256 = "db1744578d50779069007216c5c8f359392d5e0e83ebe2232aa299acc8b30cb3" %} package: name: {{name}} From 2d92c47e438e7cb9354f1ad698bac18fadaebb62 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 May 2024 12:16:34 -0400 Subject: [PATCH 79/81] Update jcvi to 1.4.11 (#47821) Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com> --- recipes/jcvi/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/jcvi/meta.yaml b/recipes/jcvi/meta.yaml index 74e4055bb11ca7..182269b6c3e2d4 100644 --- a/recipes/jcvi/meta.yaml +++ b/recipes/jcvi/meta.yaml @@ -1,5 +1,5 @@ {% set name = "jcvi" %} -{% set version = "1.4.10" %} +{% set version = "1.4.11" %} package: name: {{ name }} @@ -7,7 +7,7 @@ package: source: url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz - sha256: 3c9763e6dbe3a85bc9f66f835814edaaf2929142179dc03f5a79536358117026 + sha256: 7f9090d1218cbe2bfe05fdaccdcf1c813e86bc8da6e7ac37330172a70fb3364f build: skip: True # [osx] From 10cfea02580babb9dd7ead9a08585e47cce4a0e6 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Fri, 10 May 2024 12:16:42 -0400 Subject: [PATCH 80/81] Update thermorawfileparser to 1.4.4 (#47823) --- recipes/thermorawfileparser/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/thermorawfileparser/meta.yaml b/recipes/thermorawfileparser/meta.yaml index 6021696b4411bd..13b3928df5f636 100644 --- a/recipes/thermorawfileparser/meta.yaml +++ b/recipes/thermorawfileparser/meta.yaml @@ -1,5 +1,5 @@ {% set name = "ThermoRawFileParser" %} -{% set version = "1.4.3" %} +{% set version = "1.4.4" %} package: name: {{ name|lower }} @@ -21,7 +21,7 @@ build: source: # downloading pre-compiled packages, msbuild is a hell to compile under Linux url: https://github.com/compomics/ThermoRawFileParser/releases/download/v{{ version }}/ThermoRawFileParser{{ version }}.zip - sha256: 4643347d5486e1dec89d1fd2742920661ae6a6d099a974652a5d9b3b15a26155 + sha256: 5fff9266636422557095b5eea0a18b26f5a9972f49a538d93cb969a6b239a044 requirements: build: From 957c6af989e3f05fc3e401ee3a3526ae788b573f Mon Sep 17 00:00:00 2001 From: Carl Mathias Kobel Date: Sun, 12 May 2024 15:39:27 +0200 Subject: [PATCH 81/81] Add Gapseq (#47417) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * init * passes bioconda-utils lint * works too * polishing * final test * ensure correct pinning * minor tweaks * test was too long. * amend * work on tests after package has been published * updates according to bgruening's comments * r-chnosz is now available on conda-forge * amend * reset build number * Update recipes/gapseq/meta.yaml Co-authored-by: Björn Grüning --------- Co-authored-by: Björn Grüning --- recipes/gapseq/build.sh | 41 +++++++++++++++++++++++ recipes/gapseq/meta.yaml | 71 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 112 insertions(+) create mode 100644 recipes/gapseq/build.sh create mode 100644 recipes/gapseq/meta.yaml diff --git a/recipes/gapseq/build.sh b/recipes/gapseq/build.sh new file mode 100644 index 00000000000000..5cf8ec2bdb7b90 --- /dev/null +++ b/recipes/gapseq/build.sh @@ -0,0 +1,41 @@ +#!/usr/bin/env bash + +# Installation instructions taken from https://github.com/jotech/gapseq/blob/master/docs/install.md#conda April 2024 by cmkobel + +# Copy contents to conda prefix +mkdir -p ${PREFIX}/gapseq/ +cp ISSUE_TEMPLATE.MD LICENSE README.md gapseq gapseq_env.yml ${PREFIX}/gapseq/ +cp -r dat/ docs/ src/ toy/ unit/ ${PREFIX}/gapseq/ + + +# Installing the CRAN archived sybilSBML package here requires a bunch of debugging to set the lib paths in R. That time is probably better spend fixing the package (sybilSBML) in the first place. So here is a quick workaround that makes this process a bit easier for the user. SybilSBML is not strictly necessary so I think the priority should be to get the main package (gapseq) working first. +echo '''#!/usr/bin/env bash +wget https://cran.r-project.org/src/contrib/Archive/sybilSBML/sybilSBML_3.1.2.tar.gz +R CMD INSTALL --configure-args=" \ +--with-sbml-include=$CONDA_PREFIX/include \ +--with-sbml-lib=$CONDA_PREFIX/lib" sybilSBML_3.1.2.tar.gz +rm sybilSBML_3.1.2.tar.gz +''' > ${PREFIX}/gapseq/src/install_archived_sybilSBML.sh +chmod +x ${PREFIX}/gapseq/src/install_archived_sybilSBML.sh +# Now the user can "easily" install this after installing the bioconda package with install_archived_sybilSBML.sh (This file will be linked to bin/). + + +# Download reference sequence data +# To install the database, we must call the installed file as it uses its own path to place the files correctly. +bash ${PREFIX}/gapseq/src/update_sequences.sh + + +# Final setup - Make binary available +mkdir -p ${PREFIX}/bin +ln -sr ${PREFIX}/gapseq/gapseq ${PREFIX}/bin/ +ln -sr ${PREFIX}/gapseq/src/update_sequences.sh ${PREFIX}/bin/ +ln -sr ${PREFIX}/gapseq/src/install_archived_sybilSBML.sh ${PREFIX}/bin/ + + +# --- + + +# Build at home with (before submitting to azure): +# conda activate bioconda-utils +# bioconda-utils lint --git-range master +# bioconda-utils build --mulled-test --git-range master diff --git a/recipes/gapseq/meta.yaml b/recipes/gapseq/meta.yaml new file mode 100644 index 00000000000000..b62b67d0b87553 --- /dev/null +++ b/recipes/gapseq/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.2" %} + +package: + name: gapseq + version: {{ version }} + +source: + url: https://github.com/jotech/gapseq/archive/refs/tags/v{{ version}}.tar.gz + sha256: 061799f8e0406662450dd3d8d61d824220670fb23231895deecd490a5cbdf7cf + +build: + number: 0 + run_exports: + - {{ pin_subpackage('gapseq', max_pin="x") }} + skip: True # [osx] + +requirements: + run: + - r-base + - perl + - parallel + - gawk + - sed + - grep + - bc + - git + - coreutils + - wget + - openssl + - barrnap + - bedtools + - exonerate + - glpk + - hmmer + - blast + - libsbml + - r-data.table + - r-stringr + - r-stringi + - r-getopt + - r-doParallel + - r-foreach + - r-r.utils + - r-sybil + - r-biocmanager + - bioconductor-biostrings + - r-jsonlite + - r-renv + - r-glpkapi + - r-rcurl + - r-httr + - r-chnosz + build: + - wget + +test: + commands: + - gapseq test + +about: + home: https://github.com/jotech/gapseq + summary: Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks + license_family: GPL + license: AGPL-3.0-only + license_file: LICENSE +extra: + skip-lints: + - should_be_noarch_generic + recipe-maintainers: + - cmkobel +