From 39a973fd18d4421627700fc3067797388f3aba1b Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Wed, 27 Mar 2024 14:16:02 +0200 Subject: [PATCH 01/10] medaka: add linux-aarch64 build Signed-off-by: Martin Tzvetanov Grigorov --- recipes/medaka/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 39da07aeeb982..bbf365eb5a8cc 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -14,7 +14,7 @@ source: - patch build: - number: 0 + number: 1 entry_points: - medaka = medaka.medaka:main - medaka_counts = medaka.medaka_counts:main @@ -33,7 +33,7 @@ requirements: - cffi >=1.15.0 - htslib >=1.14 - libcurl - - openssl + - openssl >=1.1.1 - bzip2 - xz - zlib @@ -61,7 +61,7 @@ requirements: - minimap2 >=2.17 - htslib >=1.14 - libcurl - - openssl + - openssl >=1.1.1 - wurlitzer test: @@ -82,6 +82,8 @@ about: dev_url: https://github.com/nanoporetech/medaka extra: + additional-platforms: + - linux-aarch64 identifiers: - usegalaxy-eu:medaka_consensus - biotools:medaka From fb4aafe8732fc0082c7280264e9b3cd23a2df945 Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Wed, 27 Mar 2024 14:39:07 +0200 Subject: [PATCH 02/10] Try with libcurl >=8.6.0 (latest available) The build currently fails with: ``` The reported errors are: - Encountered problems while solving: - - nothing provides openssl >=1.0.2p,<1.0.3a needed by libcurl-7.63.0-h01ee5af_1000 - ``` Signed-off-by: Martin Tzvetanov Grigorov --- recipes/medaka/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index bbf365eb5a8cc..ce78e49a1997c 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -32,7 +32,7 @@ requirements: - pip - cffi >=1.15.0 - htslib >=1.14 - - libcurl + - libcurl >=8.6.0 - openssl >=1.1.1 - bzip2 - xz @@ -60,7 +60,7 @@ requirements: - bcftools >=1.14 - minimap2 >=2.17 - htslib >=1.14 - - libcurl + - libcurl >=8.6.0 - openssl >=1.1.1 - wurlitzer From 4b800c1a048dc458b2342af9c8943c788b6ee8a5 Mon Sep 17 00:00:00 2001 From: mencian Date: Wed, 8 May 2024 21:40:30 -0500 Subject: [PATCH 03/10] clean up recipe --- recipes/medaka/LICENSE.md | 364 -------------------------------------- recipes/medaka/build.sh | 4 +- recipes/medaka/meta.yaml | 15 +- 3 files changed, 10 insertions(+), 373 deletions(-) delete mode 100644 recipes/medaka/LICENSE.md diff --git a/recipes/medaka/LICENSE.md b/recipes/medaka/LICENSE.md deleted file mode 100644 index 56dddbbdb5f2d..0000000000000 --- a/recipes/medaka/LICENSE.md +++ /dev/null @@ -1,364 +0,0 @@ -This Source Code Form is subject to the terms of the Mozilla Public -License, v. 2.0. If a copy of the MPL was not distributed with this -file, You can obtain one at http://mozilla.org/MPL/2.0/. - -(c) 2016 Oxford Nanopore Technologies Ltd. - - -Mozilla Public License Version 2.0 -================================== - -### 1. Definitions - -**1.1. “Contributor”** - means each individual or legal entity that creates, contributes to - the creation of, or owns Covered Software. - -**1.2. “Contributor Version”** - means the combination of the Contributions of others (if any) used - by a Contributor and that particular Contributor's Contribution. - -**1.3. “Contribution”** - means Covered Software of a particular Contributor. - -**1.4. “Covered Software”** - means Source Code Form to which the initial Contributor has attached - the notice in Exhibit A, the Executable Form of such Source Code - Form, and Modifications of such Source Code Form, in each case - including portions thereof. - -**1.5. “Incompatible With Secondary Licenses”** - means - -* **(a)** that the initial Contributor has attached the notice described - in Exhibit B to the Covered Software; or -* **(b)** that the Covered Software was made available under the terms of - version 1.1 or earlier of the License, but not also under the - terms of a Secondary License. - -**1.6. “Executable Form”** - means any form of the work other than Source Code Form. - -**1.7. “Larger Work”** - means a work that combines Covered Software with other material, in - a separate file or files, that is not Covered Software. - -**1.8. “License”** - means this document. - -**1.9. “Licensable”** - means having the right to grant, to the maximum extent possible, - whether at the time of the initial grant or subsequently, any and - all of the rights conveyed by this License. - -**1.10. “Modifications”** - means any of the following: - -* **(a)** any file in Source Code Form that results from an addition to, - deletion from, or modification of the contents of Covered - Software; or -* **(b)** any new file in Source Code Form that contains any Covered - Software. - -**1.11. “Patent Claims” of a Contributor** - means any patent claim(s), including without limitation, method, - process, and apparatus claims, in any patent Licensable by such - Contributor that would be infringed, but for the grant of the - License, by the making, using, selling, offering for sale, having - made, import, or transfer of either its Contributions or its - Contributor Version. - -**1.12. “Secondary License”** - means either the GNU General Public License, Version 2.0, the GNU - Lesser General Public License, Version 2.1, the GNU Affero General - Public License, Version 3.0, or any later versions of those - licenses. - -**1.13. “Source Code Form”** - means the form of the work preferred for making modifications. - -**1.14. “You” (or “Your”)** - means an individual or a legal entity exercising rights under this - License. For legal entities, “You” includes any entity that - controls, is controlled by, or is under common control with You. For - purposes of this definition, “control” means **(a)** the power, direct - or indirect, to cause the direction or management of such entity, - whether by contract or otherwise, or **(b)** ownership of more than - fifty percent (50%) of the outstanding shares or beneficial - ownership of such entity. - - -### 2. License Grants and Conditions - -#### 2.1. Grants - -Each Contributor hereby grants You a world-wide, royalty-free, -non-exclusive license: - -* **(a)** under intellectual property rights (other than patent or trademark) - Licensable by such Contributor to use, reproduce, make available, - modify, display, perform, distribute, and otherwise exploit its - Contributions, either on an unmodified basis, with Modifications, or - as part of a Larger Work; and -* **(b)** under Patent Claims of such Contributor to make, use, sell, offer - for sale, have made, import, and otherwise transfer either its - Contributions or its Contributor Version. - -#### 2.2. Effective Date - -The licenses granted in Section 2.1 with respect to any Contribution -become effective for each Contribution on the date the Contributor first -distributes such Contribution. - -#### 2.3. Limitations on Grant Scope - -The licenses granted in this Section 2 are the only rights granted under -this License. No additional rights or licenses will be implied from the -distribution or licensing of Covered Software under this License. -Notwithstanding Section 2.1(b) above, no patent license is granted by a -Contributor: - -* **(a)** for any code that a Contributor has removed from Covered Software; - or -* **(b)** for infringements caused by: **(i)** Your and any other third party's - modifications of Covered Software, or **(ii)** the combination of its - Contributions with other software (except as part of its Contributor - Version); or -* **(c)** under Patent Claims infringed by Covered Software in the absence of - its Contributions. - -This License does not grant any rights in the trademarks, service marks, -or logos of any Contributor (except as may be necessary to comply with -the notice requirements in Section 3.4). - -#### 2.4. Subsequent Licenses - -No Contributor makes additional grants as a result of Your choice to -distribute the Covered Software under a subsequent version of this -License (see Section 10.2) or under the terms of a Secondary License (if -permitted under the terms of Section 3.3). - -#### 2.5. Representation - -Each Contributor represents that the Contributor believes its -Contributions are its original creation(s) or it has sufficient rights -to grant the rights to its Contributions conveyed by this License. - -#### 2.6. Fair Use - -This License is not intended to limit any rights You have under -applicable copyright doctrines of fair use, fair dealing, or other -equivalents. - -#### 2.7. Conditions - -Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted -in Section 2.1. - - -### 3. Responsibilities - -#### 3.1. Distribution of Source Form - -All distribution of Covered Software in Source Code Form, including any -Modifications that You create or to which You contribute, must be under -the terms of this License. You must inform recipients that the Source -Code Form of the Covered Software is governed by the terms of this -License, and how they can obtain a copy of this License. You may not -attempt to alter or restrict the recipients' rights in the Source Code -Form. - -#### 3.2. Distribution of Executable Form - -If You distribute Covered Software in Executable Form then: - -* **(a)** such Covered Software must also be made available in Source Code - Form, as described in Section 3.1, and You must inform recipients of - the Executable Form how they can obtain a copy of such Source Code - Form by reasonable means in a timely manner, at a charge no more - than the cost of distribution to the recipient; and - -* **(b)** You may distribute such Executable Form under the terms of this - License, or sublicense it under different terms, provided that the - license for the Executable Form does not attempt to limit or alter - the recipients' rights in the Source Code Form under this License. - -#### 3.3. Distribution of a Larger Work - -You may create and distribute a Larger Work under terms of Your choice, -provided that You also comply with the requirements of this License for -the Covered Software. If the Larger Work is a combination of Covered -Software with a work governed by one or more Secondary Licenses, and the -Covered Software is not Incompatible With Secondary Licenses, this -License permits You to additionally distribute such Covered Software -under the terms of such Secondary License(s), so that the recipient of -the Larger Work may, at their option, further distribute the Covered -Software under the terms of either this License or such Secondary -License(s). - -#### 3.4. Notices - -You may not remove or alter the substance of any license notices -(including copyright notices, patent notices, disclaimers of warranty, -or limitations of liability) contained within the Source Code Form of -the Covered Software, except that You may alter any license notices to -the extent required to remedy known factual inaccuracies. - -#### 3.5. Application of Additional Terms - -You may choose to offer, and to charge a fee for, warranty, support, -indemnity or liability obligations to one or more recipients of Covered -Software. However, You may do so only on Your own behalf, and not on -behalf of any Contributor. You must make it absolutely clear that any -such warranty, support, indemnity, or liability obligation is offered by -You alone, and You hereby agree to indemnify every Contributor for any -liability incurred by such Contributor as a result of warranty, support, -indemnity or liability terms You offer. You may include additional -disclaimers of warranty and limitations of liability specific to any -jurisdiction. - - -### 4. Inability to Comply Due to Statute or Regulation - -If it is impossible for You to comply with any of the terms of this -License with respect to some or all of the Covered Software due to -statute, judicial order, or regulation then You must: **(a)** comply with -the terms of this License to the maximum extent possible; and **(b)** -describe the limitations and the code they affect. Such description must -be placed in a text file included with all distributions of the Covered -Software under this License. Except to the extent prohibited by statute -or regulation, such description must be sufficiently detailed for a -recipient of ordinary skill to be able to understand it. - - -### 5. Termination - -**5.1.** The rights granted under this License will terminate automatically -if You fail to comply with any of its terms. However, if You become -compliant, then the rights granted under this License from a particular -Contributor are reinstated **(a)** provisionally, unless and until such -Contributor explicitly and finally terminates Your grants, and **(b)** on an -ongoing basis, if such Contributor fails to notify You of the -non-compliance by some reasonable means prior to 60 days after You have -come back into compliance. Moreover, Your grants from a particular -Contributor are reinstated on an ongoing basis if such Contributor -notifies You of the non-compliance by some reasonable means, this is the -first time You have received notice of non-compliance with this License -from such Contributor, and You become compliant prior to 30 days after -Your receipt of the notice. - -**5.2.** If You initiate litigation against any entity by asserting a patent -infringement claim (excluding declaratory judgment actions, -counter-claims, and cross-claims) alleging that a Contributor Version -directly or indirectly infringes any patent, then the rights granted to -You by any and all Contributors for the Covered Software under Section -2.1 of this License shall terminate. - -**5.3.** In the event of termination under Sections 5.1 or 5.2 above, all -end user license agreements (excluding distributors and resellers) which -have been validly granted by You or Your distributors under this License -prior to termination shall survive termination. - - -### 6. Disclaimer of Warranty - -> Covered Software is provided under this License on an “as is” -> basis, without warranty of any kind, either expressed, implied, or -> statutory, including, without limitation, warranties that the -> Covered Software is free of defects, merchantable, fit for a -> particular purpose or non-infringing. The entire risk as to the -> quality and performance of the Covered Software is with You. -> Should any Covered Software prove defective in any respect, You -> (not any Contributor) assume the cost of any necessary servicing, -> repair, or correction. This disclaimer of warranty constitutes an -> essential part of this License. No use of any Covered Software is -> authorized under this License except under this disclaimer. - -### 7. Limitation of Liability - -> Under no circumstances and under no legal theory, whether tort -> (including negligence), contract, or otherwise, shall any -> Contributor, or anyone who distributes Covered Software as -> permitted above, be liable to You for any direct, indirect, -> special, incidental, or consequential damages of any character -> including, without limitation, damages for lost profits, loss of -> goodwill, work stoppage, computer failure or malfunction, or any -> and all other commercial damages or losses, even if such party -> shall have been informed of the possibility of such damages. This -> limitation of liability shall not apply to liability for death or -> personal injury resulting from such party's negligence to the -> extent applicable law prohibits such limitation. Some -> jurisdictions do not allow the exclusion or limitation of -> incidental or consequential damages, so this exclusion and -> limitation may not apply to You. - - -### 8. Litigation - -Any litigation relating to this License may be brought only in the -courts of a jurisdiction where the defendant maintains its principal -place of business and such litigation shall be governed by laws of that -jurisdiction, without reference to its conflict-of-law provisions. -Nothing in this Section shall prevent a party's ability to bring -cross-claims or counter-claims. - - -### 9. Miscellaneous - -This License represents the complete agreement concerning the subject -matter hereof. If any provision of this License is held to be -unenforceable, such provision shall be reformed only to the extent -necessary to make it enforceable. Any law or regulation which provides -that the language of a contract shall be construed against the drafter -shall not be used to construe this License against a Contributor. - - -### 10. Versions of the License - -#### 10.1. New Versions - -Mozilla Foundation is the license steward. Except as provided in Section -10.3, no one other than the license steward has the right to modify or -publish new versions of this License. Each version will be given a -distinguishing version number. - -#### 10.2. Effect of New Versions - -You may distribute the Covered Software under the terms of the version -of the License under which You originally received the Covered Software, -or under the terms of any subsequent version published by the license -steward. - -#### 10.3. Modified Versions - -If you create software not governed by this License, and you want to -create a new license for such software, you may create and use a -modified version of this License if you rename the license and remove -any references to the name of the license steward (except to note that -such modified license differs from this License). - -#### 10.4. Distributing Source Code Form that is Incompatible With Secondary Licenses - -If You choose to distribute Source Code Form that is Incompatible With -Secondary Licenses under the terms of this version of the License, the -notice described in Exhibit B of this License must be attached. - -## Exhibit A - Source Code Form License Notice - - This Source Code Form is subject to the terms of the Mozilla Public - License, v. 2.0. If a copy of the MPL was not distributed with this - file, You can obtain one at http://mozilla.org/MPL/2.0/. - -If it is not possible or desirable to put the notice in a particular -file, then You may include the notice in a location (such as a LICENSE -file in a relevant directory) where a recipient would be likely to look -for such a notice. - -You may add additional accurate notices of copyright ownership. - -## Exhibit B - “Incompatible With Secondary Licenses” Notice - - This Source Code Form is "Incompatible With Secondary Licenses", as - defined by the Mozilla Public License, v. 2.0. - - diff --git a/recipes/medaka/build.sh b/recipes/medaka/build.sh index a17d134c7c243..09567722151f5 100644 --- a/recipes/medaka/build.sh +++ b/recipes/medaka/build.sh @@ -4,7 +4,7 @@ export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib" -export CFLAGS="-I${PREFIX}/include ${LDFLAGS}" +export CFLAGS="${CFLAGS} -O3 -I${PREFIX}/include ${LDFLAGS}" # disable Makefile driven build of htslib.a sed -i.bak "s/'build_ext': HTSBuild//" setup.py @@ -13,4 +13,4 @@ sed -i.bak "s/'build_ext': HTSBuild//" setup.py sed -i.bak 's/extra_objects.*//' build.py sed -i.bak 's/^libraries=\[/libraries=\["hts",/' build.py -$PYTHON -m pip install . --no-deps --ignore-installed -vvv +${PYTHON} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index ce78e49a1997c..c290af9213a5d 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -1,4 +1,4 @@ -{% set name = "Medaka" %} +{% set name = "medaka" %} {% set version = "1.11.3" %} {% set sha256 = "940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9" %} # Bot PRs - Always review requirements.txt for new release @@ -8,7 +8,7 @@ package: version: {{ version }} source: - url: https://github.com/nanoporetech/medaka/releases/download/v{{ version }}/medaka-{{ version }}.tar.gz + url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/medaka-{{ version }}.tar.gz sha256: {{ sha256 }} patches: - patch @@ -74,12 +74,13 @@ test: - medaka_version_report about: - home: https://github.com/nanoporetech/medaka - summary: Neural network sequence error correction. - license: MPL-2.0 + home: "https://github.com/nanoporetech/medaka" + summary: "A tool to create consensus sequences and variant calls from nanopore sequencing data using neural networks." + license: "MPL-2.0" license_family: OTHER - license_file: LICENSE.md - dev_url: https://github.com/nanoporetech/medaka + license_file: "LICENSE.md" + dev_url: "https://github.com/nanoporetech/medaka" + doc_url: "https://github.com/nanoporetech/medaka/blob/master/README.md" extra: additional-platforms: From a7bd5a2b8418a09ff1ae3f193711579dc4e5062b Mon Sep 17 00:00:00 2001 From: mencian Date: Wed, 8 May 2024 22:10:43 -0500 Subject: [PATCH 04/10] edit build.sh --- recipes/medaka/build.sh | 2 +- recipes/medaka/meta.yaml | 6 ++---- 2 files changed, 3 insertions(+), 5 deletions(-) diff --git a/recipes/medaka/build.sh b/recipes/medaka/build.sh index 09567722151f5..a3a281e43620b 100644 --- a/recipes/medaka/build.sh +++ b/recipes/medaka/build.sh @@ -1,4 +1,4 @@ -#!/bin/bash +#!/bin/bash -euo export INCLUDE_PATH="${PREFIX}/include" export LIBRARY_PATH="${PREFIX}/lib" diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index c290af9213a5d..79d269bd9786b 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -32,8 +32,8 @@ requirements: - pip - cffi >=1.15.0 - htslib >=1.14 - - libcurl >=8.6.0 - - openssl >=1.1.1 + - libcurl + - openssl - bzip2 - xz - zlib @@ -60,8 +60,6 @@ requirements: - bcftools >=1.14 - minimap2 >=2.17 - htslib >=1.14 - - libcurl >=8.6.0 - - openssl >=1.1.1 - wurlitzer test: From 51081adf1acd4f16f08e4346e73efed5f9534ab5 Mon Sep 17 00:00:00 2001 From: mencian Date: Wed, 8 May 2024 22:17:56 -0500 Subject: [PATCH 05/10] edit meta.yaml --- recipes/medaka/meta.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 79d269bd9786b..915728636c035 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -31,7 +31,7 @@ requirements: - python - pip - cffi >=1.15.0 - - htslib >=1.14 + - htslib - libcurl - openssl - bzip2 @@ -56,10 +56,10 @@ requirements: - pysam >=0.16.0.1 - python-edlib - requests - - samtools >=1.14 - - bcftools >=1.14 + - samtools + - bcftools - minimap2 >=2.17 - - htslib >=1.14 + - htslib - wurlitzer test: From 42385b8753d95fc9245d45fa1b55aae2cfe5c31b Mon Sep 17 00:00:00 2001 From: mencian Date: Wed, 8 May 2024 22:24:53 -0500 Subject: [PATCH 06/10] edit meta.yaml --- recipes/medaka/conda_build_config.yaml | 2 +- recipes/medaka/meta.yaml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/recipes/medaka/conda_build_config.yaml b/recipes/medaka/conda_build_config.yaml index f45b292d8ac64..9a8036760d242 100644 --- a/recipes/medaka/conda_build_config.yaml +++ b/recipes/medaka/conda_build_config.yaml @@ -6,4 +6,4 @@ libcurl: - 7 openssl: - - 1.1.1 + - 1.0.2u diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 915728636c035..79d269bd9786b 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -31,7 +31,7 @@ requirements: - python - pip - cffi >=1.15.0 - - htslib + - htslib >=1.14 - libcurl - openssl - bzip2 @@ -56,10 +56,10 @@ requirements: - pysam >=0.16.0.1 - python-edlib - requests - - samtools - - bcftools + - samtools >=1.14 + - bcftools >=1.14 - minimap2 >=2.17 - - htslib + - htslib >=1.14 - wurlitzer test: From ea8ba27c4a50850b1084bd63e481a2cdd2499ec9 Mon Sep 17 00:00:00 2001 From: mencian Date: Wed, 8 May 2024 22:38:15 -0500 Subject: [PATCH 07/10] edit meta.yaml --- recipes/medaka/conda_build_config.yaml | 2 +- recipes/medaka/meta.yaml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/recipes/medaka/conda_build_config.yaml b/recipes/medaka/conda_build_config.yaml index 9a8036760d242..f45b292d8ac64 100644 --- a/recipes/medaka/conda_build_config.yaml +++ b/recipes/medaka/conda_build_config.yaml @@ -6,4 +6,4 @@ libcurl: - 7 openssl: - - 1.0.2u + - 1.1.1 diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index 79d269bd9786b..e136f4e9faa2e 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -31,7 +31,7 @@ requirements: - python - pip - cffi >=1.15.0 - - htslib >=1.14 + #- htslib >=1.14 - libcurl - openssl - bzip2 @@ -57,9 +57,9 @@ requirements: - python-edlib - requests - samtools >=1.14 - - bcftools >=1.14 + #- bcftools >=1.14 - minimap2 >=2.17 - - htslib >=1.14 + #- htslib >=1.14 - wurlitzer test: From cac9d21bd6cbbc6286da075226d1ea5d1eb1ed69 Mon Sep 17 00:00:00 2001 From: mencian Date: Mon, 13 May 2024 05:47:01 -0500 Subject: [PATCH 08/10] edit meta.yaml --- recipes/medaka/build.sh | 2 ++ recipes/medaka/meta.yaml | 11 ++++++----- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/recipes/medaka/build.sh b/recipes/medaka/build.sh index a3a281e43620b..909346d2b1f85 100644 --- a/recipes/medaka/build.sh +++ b/recipes/medaka/build.sh @@ -13,4 +13,6 @@ sed -i.bak "s/'build_ext': HTSBuild//" setup.py sed -i.bak 's/extra_objects.*//' build.py sed -i.bak 's/^libraries=\[/libraries=\["hts",/' build.py +rm -rf *.bak + ${PYTHON} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv diff --git a/recipes/medaka/meta.yaml b/recipes/medaka/meta.yaml index e136f4e9faa2e..836ba4bb2aa8f 100644 --- a/recipes/medaka/meta.yaml +++ b/recipes/medaka/meta.yaml @@ -25,13 +25,14 @@ build: requirements: build: - - {{ compiler('c') }} - - coreutils + - {{ compiler('cxx') }} + - make + - cmake host: - python - pip - cffi >=1.15.0 - #- htslib >=1.14 + - htslib >=1.14 - libcurl - openssl - bzip2 @@ -57,9 +58,9 @@ requirements: - python-edlib - requests - samtools >=1.14 - #- bcftools >=1.14 + - bcftools >=1.14 - minimap2 >=2.17 - #- htslib >=1.14 + - htslib >=1.14 - wurlitzer test: From 259f715393b4affce8d6516cd44588cb5ddd6321 Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Mon, 13 May 2024 14:51:00 +0300 Subject: [PATCH 09/10] Try with libcurl 8.x in conda_build_config.yaml Signed-off-by: Martin Tzvetanov Grigorov --- recipes/medaka/conda_build_config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/medaka/conda_build_config.yaml b/recipes/medaka/conda_build_config.yaml index f45b292d8ac64..ebdb42545873b 100644 --- a/recipes/medaka/conda_build_config.yaml +++ b/recipes/medaka/conda_build_config.yaml @@ -4,6 +4,6 @@ # lead solver conflicts in the future. Please review this on future # releases, especially if support for TensorFlow 2.11+ is added. libcurl: - - 7 + - 8 openssl: - 1.1.1 From d9a796700d865402b03bccf5b2081f22b35eb1ef Mon Sep 17 00:00:00 2001 From: Martin Tzvetanov Grigorov Date: Mon, 13 May 2024 15:11:50 +0300 Subject: [PATCH 10/10] Try with openssl 3.x in conda_build_config.yaml Signed-off-by: Martin Tzvetanov Grigorov --- recipes/medaka/conda_build_config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/medaka/conda_build_config.yaml b/recipes/medaka/conda_build_config.yaml index ebdb42545873b..c11925f3b0d84 100644 --- a/recipes/medaka/conda_build_config.yaml +++ b/recipes/medaka/conda_build_config.yaml @@ -6,4 +6,4 @@ libcurl: - 8 openssl: - - 1.1.1 + - 3