From 54d32148cc1ad082e414996050c83df23081e60d Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 15 Oct 2024 00:31:15 +0200 Subject: [PATCH 01/34] adding easyconfigs: Anaconda3-2024.06-1.eb --- .../a/Anaconda3/Anaconda3-2024.06-1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb new file mode 100644 index 00000000000..674a7cc8fd6 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.06-1.eb @@ -0,0 +1,33 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, +# 2019.10, 2020.2, 2020.11, 2022.05, +# 2022.10, 2024.2-1 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +# config upgrade to 2023.09 by Sarah Walters + +# no support for power architecture in 2024.02-1 on https://repo.anaconda.com/archive/, as off 13 Feb 2024 +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2024.06-1' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': '539bb43d9a52d758d0fdfa1b1b049920ec6f8c6d15ee9fe4a423355fe551a8f7', + '%(name)s-%(version)s-Linux-aarch64.sh': 'b4be0ad2052236882402902a31d32cd37635d3db194a42f977be0d68a8ff1a31', + } +] + +moduleclass = 'lang' From 4cb831f5c59a3592c0c9c58701da13c68d22f36b Mon Sep 17 00:00:00 2001 From: software Date: Thu, 31 Oct 2024 17:00:01 +0000 Subject: [PATCH 02/34] adding easyconfigs: Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb, prokka-1.14.5-gompi-2023a.eb --- .../Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb | 28 +++++++++++ .../p/prokka/prokka-1.14.5-gompi-2023a.eb | 50 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb new file mode 100644 index 00000000000..8c8af50568f --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.36.1'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb new file mode 100644 index 00000000000..05fe75468f6 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.14.1'), + ('Java', '11', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20230722'), + ('tbl2asn', '20230713', '-linux64', SYSTEM), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' From 1b20d6213750892c45ff16b5e515dda355df636e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 18 Nov 2024 15:33:16 +0100 Subject: [PATCH 03/34] adding easyconfigs: bin2cell-0.3.2-foss-2023a.eb, fastparquet-2024.11.0-gfbf-2023a.eb, stardist-0.8.5-foss-2023a.eb --- .../b/bin2cell/bin2cell-0.3.2-foss-2023a.eb | 37 +++++ .../fastparquet-2024.11.0-gfbf-2023a.eb | 146 ++++++++++++++++++ .../s/stardist/stardist-0.8.5-foss-2023a.eb | 37 +++++ 3 files changed, 220 insertions(+) create mode 100644 easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb b/easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb new file mode 100644 index 00000000000..85e6f82cb90 --- /dev/null +++ b/easybuild/easyconfigs/b/bin2cell/bin2cell-0.3.2-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'bin2cell' +version = '0.3.2' + +homepage = 'https://github.com/Teichlab/bin2cell' +description = """Bin2cell proposes 2um bin to cell groupings based on segmentation, +which can be done on the morphology image and/or a visualisation of the gene expression.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scanpy', '1.9.8'), + ('OpenCV', '4.8.1', '-contrib'), + ('stardist', '0.8.5'), + ('fastparquet', '2024.11.0'), +] + +exts_list = [ + ('flit_core', '3.9.0', { + 'checksums': ['72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba'], + }), + (name, version, { + # opencv-python is installed via OpenCV, python module name is 'cv2' + 'preinstallopts': "sed -i '/opencv-python/d' pyproject.toml &&", + 'checksums': ['6529a8260b75c8c0237938f4ea389dfe055aea0909a31315f8fec32d44b2c531'], + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['python -c "import cv2"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb new file mode 100644 index 00000000000..0aa5903ee6e --- /dev/null +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb @@ -0,0 +1,146 @@ +easyblock = 'CargoPythonBundle' + +name = 'fastparquet' +version = '2024.11.0' + +homepage = "https://fastparquet.readthedocs.io/" +description = """fastparquet is a python implementation of the parquet format, aiming to integrate +into python-based big data work-flows. It is used implicitly by the projects +Dask, Pandas and intake-parquet.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('Autotools', '20220317'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('NASM', '2.16.01'), +] + +crates = [ + ('adler2', '2.0.0'), + ('alloc-no-stdlib', '2.0.4'), + ('alloc-stdlib', '0.2.2'), + ('atty', '0.2.14'), + ('autocfg', '1.4.0'), + ('bitflags', '1.3.2'), + ('bitflags', '2.6.0'), + ('blosc2-rs', '0.3.1+2.15.1'), + ('blosc2-sys', '0.3.1+2.15.1'), + ('brotli', '7.0.0'), + ('brotli-decompressor', '4.0.1'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cbindgen', '0.24.5'), + ('cc', '1.1.30'), + ('cfg-if', '1.0.0'), + ('clap', '3.2.25'), + ('clap_lex', '0.2.4'), + ('cmake', '0.1.51'), + ('copy_dir', '0.1.3'), + ('crc32fast', '1.4.2'), + ('errno', '0.3.9'), + ('fastrand', '2.1.1'), + ('flate2', '1.0.34'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.1.19'), + ('indexmap', '1.9.3'), + ('indoc', '2.0.5'), + ('isal-rs', '0.5.3+496255c'), + ('isal-sys', '0.5.3+496255c'), + ('itoa', '1.0.11'), + ('jobserver', '0.1.32'), + ('libc', '0.2.159'), + ('libcramjam', '0.6.0'), + ('libdeflate-sys', '1.19.3'), + ('libdeflater', '1.19.3'), + ('linux-raw-sys', '0.4.14'), + ('lock_api', '0.4.12'), + ('log', '0.4.22'), + ('lz4', '1.28.0'), + ('lz4-sys', '1.11.1+lz4-1.10.0'), + ('lzma-sys', '0.1.20'), + ('memchr', '2.7.4'), + ('memoffset', '0.9.1'), + ('miniz_oxide', '0.8.0'), + ('once_cell', '1.20.2'), + ('os_str_bytes', '6.6.1'), + ('parking_lot', '0.12.3'), + ('parking_lot_core', '0.9.10'), + ('pkg-config', '0.3.31'), + ('portable-atomic', '1.9.0'), + ('proc-macro2', '1.0.87'), + ('pyo3', '0.22.5'), + ('pyo3-build-config', '0.22.5'), + ('pyo3-ffi', '0.22.5'), + ('pyo3-macros', '0.22.5'), + ('pyo3-macros-backend', '0.22.5'), + ('python3-dll-a', '0.2.10'), + ('quote', '1.0.37'), + ('redox_syscall', '0.5.7'), + ('rustix', '0.38.37'), + ('ryu', '1.0.18'), + ('same-file', '1.0.6'), + ('scopeguard', '1.2.0'), + ('serde', '1.0.210'), + ('serde_derive', '1.0.210'), + ('serde_json', '1.0.128'), + ('shlex', '1.3.0'), + ('smallvec', '1.13.2'), + ('snap', '1.1.1'), + ('strsim', '0.10.0'), + ('syn', '1.0.109'), + ('syn', '2.0.79'), + ('target-lexicon', '0.12.16'), + ('tempfile', '3.13.0'), + ('termcolor', '1.4.1'), + ('textwrap', '0.16.1'), + ('toml', '0.5.11'), + ('unicode-ident', '1.0.13'), + ('unindent', '0.2.3'), + ('walkdir', '2.5.0'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.9'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('xz2', '0.1.7'), + ('zstd', '0.13.2'), + ('zstd-safe', '7.2.1'), + ('zstd-sys', '2.0.13+zstd.1.5.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('thrift', '0.21.0', { + 'checksums': ['5e6f7c50f936ebfa23e924229afc95eb219f8c8e5a83202dd4a391244803e402'], + }), + ('cramjam', '2.9.0', { + 'checksums': ['f103e648aa3ebe9b8e2c1a3a92719288d8f3f41007c319ad298cdce2d0c28641'], + }), + (name, version, { + 'checksums': ['e3b1fc73fd3e1b70b0de254bae7feb890436cb67e99458b88cb9bd3cc44db419'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb b/easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb new file mode 100644 index 00000000000..de10882b67d --- /dev/null +++ b/easybuild/easyconfigs/s/stardist/stardist-0.8.5-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'stardist' +version = '0.8.5' + +homepage = 'https://github.com/stardist/stardist' +description = "Object Detection with Star-convex Shapes." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['260a31df86ca711e5e98cb91597c6cb9a10dcd1dc3c6b826d41b7c73c9646a1e'] + +dependencies = [ + ('Python', '3.11.3'), + ('TensorFlow', '2.13.0'), + ('numba', '0.58.1'), + ('scikit-image', '0.22.0'), + ('imageio', '2.33.1'), + ('CSBDeep', '0.7.4'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/stardist-predict2d', 'bin/stardist-predict3d'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "stardist-predict2d --help", + "stardist-predict3d --help", +] + +moduleclass = 'vis' From b22f9840a7aacca926d8c0101189d974bc7393a4 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 18 Nov 2024 16:35:50 +0100 Subject: [PATCH 04/34] add checksums to fastparquet ec --- .../fastparquet-2024.11.0-gfbf-2023a.eb | 106 ++++++++++++++++++ 1 file changed, 106 insertions(+) diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb index 0aa5903ee6e..74a3177e8c3 100644 --- a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb @@ -143,4 +143,110 @@ exts_list = [ }), ] +checksums = [ + {'fastparquet-2024.11.0.tar.gz': 'e3b1fc73fd3e1b70b0de254bae7feb890436cb67e99458b88cb9bd3cc44db419'}, + {'adler2-2.0.0.tar.gz': '512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627'}, + {'alloc-no-stdlib-2.0.4.tar.gz': 'cc7bb162ec39d46ab1ca8c77bf72e890535becd1751bb45f64c597edb4c8c6b3'}, + {'alloc-stdlib-0.2.2.tar.gz': '94fb8275041c72129eb51b7d0322c29b8387a0386127718b096429201a5d6ece'}, + {'atty-0.2.14.tar.gz': 'd9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8'}, + {'autocfg-1.4.0.tar.gz': 'ace50bade8e6234aa140d9a2f552bbee1db4d353f69b8217bc503490fc1a9f26'}, + {'bitflags-1.3.2.tar.gz': 'bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a'}, + {'bitflags-2.6.0.tar.gz': 'b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de'}, + {'blosc2-rs-0.3.1+2.15.1.tar.gz': 'f35b12fa9d4360d141ea4d445661eaaa10339c89f3d3c788395cb9cad09e564a'}, + {'blosc2-sys-0.3.1+2.15.1.tar.gz': 'bc834b0173a2815db1d366bf248cd3fefdc4302910e82b852497c28463dbda6a'}, + {'brotli-7.0.0.tar.gz': 'cc97b8f16f944bba54f0433f07e30be199b6dc2bd25937444bbad560bcea29bd'}, + {'brotli-decompressor-4.0.1.tar.gz': '9a45bd2e4095a8b518033b128020dd4a55aab1c0a381ba4404a472630f4bc362'}, + {'bzip2-0.4.4.tar.gz': 'bdb116a6ef3f6c3698828873ad02c3014b3c85cadb88496095628e3ef1e347f8'}, + {'bzip2-sys-0.1.11+1.0.8.tar.gz': '736a955f3fa7875102d57c82b8cac37ec45224a07fd32d58f9f7a186b6cd4cdc'}, + {'cbindgen-0.24.5.tar.gz': 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'29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.9.tar.gz': 'cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-sys-0.59.0.tar.gz': '1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'xz2-0.1.7.tar.gz': '388c44dc09d76f1536602ead6d325eb532f5c122f17782bd57fb47baeeb767e2'}, + {'zstd-0.13.2.tar.gz': 'fcf2b778a664581e31e389454a7072dab1647606d44f7feea22cd5abb9c9f3f9'}, + {'zstd-safe-7.2.1.tar.gz': '54a3ab4db68cea366acc5c897c7b4d4d1b8994a9cd6e6f841f8964566a419059'}, + {'zstd-sys-2.0.13+zstd.1.5.6.tar.gz': '38ff0f21cfee8f97d94cef41359e0c89aa6113028ab0291aa8ca0038995a95aa'}, +] + moduleclass = 'tools' From a2aa723613e290a5d9270f17f3a2e47482096edb Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 18 Nov 2024 17:04:59 +0100 Subject: [PATCH 05/34] fix fastparquet checksums --- .../f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb index 74a3177e8c3..6724da1d7f8 100644 --- a/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2024.11.0-gfbf-2023a.eb @@ -144,7 +144,6 @@ exts_list = [ ] checksums = [ - {'fastparquet-2024.11.0.tar.gz': 'e3b1fc73fd3e1b70b0de254bae7feb890436cb67e99458b88cb9bd3cc44db419'}, {'adler2-2.0.0.tar.gz': '512761e0bb2578dd7380c6baaa0f4ce03e84f95e960231d1dec8bf4d7d6e2627'}, {'alloc-no-stdlib-2.0.4.tar.gz': 'cc7bb162ec39d46ab1ca8c77bf72e890535becd1751bb45f64c597edb4c8c6b3'}, {'alloc-stdlib-0.2.2.tar.gz': '94fb8275041c72129eb51b7d0322c29b8387a0386127718b096429201a5d6ece'}, From 4726b781d911a616b7fbd6a72014b0780da1ff63 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 21 Nov 2024 10:17:47 +0100 Subject: [PATCH 06/34] correct versions of deps --- .../d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb | 84 +++++++++++++++++++ .../git-annex-10.20240531-GCCcore-13.2.0.eb | 49 +++++++++++ .../l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb | 33 ++++++++ 3 files changed, 166 insertions(+) create mode 100644 easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..a215ceeed07 --- /dev/null +++ b/easybuild/easyconfigs/d/datalad/datalad-1.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'datalad' +version = "1.1.0" + +homepage = 'https://www.datalad.org/' +description = "DataLad is a free and open source distributed data management system that keeps track of your data, \ +creates structure, ensures reproducibility, supports collaboration, \ +and integrates with widely used data infrastructure." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), + ('poetry', '1.6.1') +] + +dependencies = [ + ('git-annex', '10.20240531'), + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('tqdm', '4.66.2'), + ('PLY', '3.11'), + ('scikit-build', '0.17.6'), +] + +use_pip = True + +exts_list = [ + ('humanize', '4.9.0', { + 'checksums': ['582a265c931c683a7e9b8ed9559089dea7edcf6cc95be39a3cbc2c5d5ac2bcfa'], + }), + ('fasteners', '0.19', { + 'checksums': ['b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c'], + }), + ('patool', '2.3.0', { + 'modulename': 'patoolib', + 'checksums': ['498e294fd8c7d50889d65019d431c6867bf3fb1fec5ea2d39d1d39d1215002f8'], + }), + ('annexremote', '1.6.5', { + 'checksums': ['ad0ccdd84a8771ad58922d172ee68b225ece77bf464abe4d24ff91a4896a423e'], + }), + ('looseversion', '1.3.0', { + 'checksums': ['ebde65f3f6bb9531a81016c6fef3eb95a61181adc47b7f949e9c0ea47911669e'], + }), + ('botocore', '1.34.121', { + 'checksums': ['1a8f94b917c47dfd84a0b531ab607dc53570efb0d073d8686600f2d2be985323'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.10.2', { + 'checksums': ['0711534e9356d3cc692fdde846b4a1e4b0cb6519971860796e6bc4c7aea00ef6'], + }), + ('boto3', '1.34.121', { + 'checksums': ['ec89f3e0b0dc959c418df29e14d3748c0b05ab7acf7c0b90c839e9f340a659fa'], + }), + ('python_gitlab', '4.5.0', { + 'modulename': 'gitlab', + 'checksums': ['0a106174949819912b9abb4232e39059f83f613177fdb1787097eb84481c64b2'], + }), + ('iso8601', '2.1.0', { + 'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'], + }), + (name, version, { + 'checksums': ['3403232696ae0e6cbcec56d7cccfac1be8b5d98f66f235e4751dd44fd9f5e8eb'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/datalad'], + 'dirs': [], +} + +sanity_check_commands = [ + "datalad --help", + "datalad --version", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..8ff1261cea3 --- /dev/null +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20240531-GCCcore-13.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'MakeCp' + +name = 'git-annex' +version = '10.20240531' + +homepage = 'https://git-annex.branchable.com' +description = """git-annex allows managing large files with git, without storing the file contents in git. It can sync, +backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the +power and distributed nature of git to bear on your large files with git-annex.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40') +] + +dependencies = [ + ('GHC', '9.10.1', '-x86_64', SYSTEM), + ('Stack', '3.1.1', '-x86_64', SYSTEM), + ('git', '2.42.0'), + ('libnsl', '2.0.1'), +] + +sources = [{ + 'git_config': {'url': 'git://git-annex.branchable.com', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s-%(version)s', + }, + 'filename': '%(name)s-%(version)s.tar.gz', +}] + +checksums = [None] + +prebuildopts = "export STACK_ROOT=$(mktemp -d) && stack setup && stack build && " +buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" + +files_to_copy = [ + (['git-annex', 'git-annex-shell'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/git-annex', 'bin/git-annex-shell'], + 'dirs': [], +} + +sanity_check_commands = ['git-annex version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d71707d2105 --- /dev/null +++ b/easybuild/easyconfigs/l/libnsl/libnsl-2.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libnsl' +version = '2.0.1' + +homepage = 'https://github.com/thkukuk/libnsl' +description = """The libnsl package contains the public client interface for NIS(YP).""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/thkukuk/%(name)s/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5c9e470b232a7acd3433491ac5221b4832f0c71318618dc6aa04dd05ffcd8fd9'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('libtirpc', '1.3.4'), +] + +# Provide a symlink for libnsl.so.1, which used to be part of glibc. +# This new version of libnsl should be backwards compatible. +postinstallcmds = ['ln -s libnsl.so %(installdir)s/lib/libnsl.so.1'] + +sanity_check_paths = { + 'files': ['include/rpcsvc/yp.h', 'lib/libnsl.a', + 'lib/libnsl.%s' % SHLIB_EXT, 'lib/libnsl.%s.1' % SHLIB_EXT], + 'dirs': ['include'] +} + +moduleclass = 'devel' From 1254d24e6a01cca6e0addf6601010b70c929f58a Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 09:53:17 +0100 Subject: [PATCH 07/34] WPS 4.6.0 WRF 4.6.1 --- .../w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb | 38 +++++ ...S-4.6.0_netCDF-Fortran_separate_path.patch | 51 ++++++ .../w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb | 44 +++++ ...F-4.6.1_netCDF-Fortran_separate_path.patch | 156 ++++++++++++++++++ 4 files changed, 289 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb new file mode 100644 index 00000000000..45612b84fa5 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb @@ -0,0 +1,38 @@ +name = 'WPS' +version = '4.6.0' + +homepage = 'https://www.mmm.ucar.edu/models/wrf' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPS-%(version)s_netCDF-Fortran_separate_path.patch', +] +checksums = [ + 'ca7bbfc6c28a107c6eb00ded70e693f5c9a3926ecde7656f49e306c9eb9a309b', # v4.6.1.tar.gz + 'ed49d5af4e6c80d9ddd9954b968c514cf888c3b35dce64744d1ac1eaa38b7042', # WPS-4.4_netCDF-Fortran_separate_path.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +builddependencies = [ + ('Perl', '5.38.2'), +] + +dependencies = [ + ('WRF', '4.6.1', versionsuffix), + ('JasPer', '4.2.4'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), + ('zlib', '1.3.1'), + ('libpng', '1.6.43'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..098eed8d7fe --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_netCDF-Fortran_separate_path.patch @@ -0,0 +1,51 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain +# updated for WPS v4.6.0 by Stefan Wolfsheimer (SURF) + + +diff -Nru WPS-4.6.0.orig/arch/preamble WPS-4.6.0/arch/preamble +--- WPS-4.6.0.orig/arch/preamble 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/arch/preamble 2024-11-29 09:25:27.634254674 +0100 +@@ -39,13 +39,14 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include \ ++ -I$(NETCDFF_DIR)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ + -L$(WRF_DIR)/external/io_int -lwrfio_int \ + -L$(WRF_DIR)/external/io_netcdf -lwrfio_nf \ +- -L$(NETCDF)/lib CONFIGURE_NETCDFF_LIB -lnetcdf ++ -L$(NETCDF)/lib -L$(NETCDFF_DIR)/lib -lnetcdff -lnetcdf + + #### Architecture specific settings #### + +diff -Nru WPS-4.6.0.orig/configure WPS-4.6.0/configure +--- WPS-4.6.0.orig/configure 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/configure 2024-11-29 09:17:10.196985634 +0100 +@@ -161,7 +161,7 @@ + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available + NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then ++ if [ -f "$NETCDFF_DIR/lib/libnetcdff.a" ] ; then + NETCDFF="-lnetcdff" + fi + else +@@ -429,9 +429,9 @@ + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` + FORMAT_FREE=`grep ^FORMAT_FREE configure.wps | cut -d"=" -f2-` + FFLAGS=`printf "%s" "${FFLAGS}" | sed -e "s/\\$(FORMAT_FREE)/${FORMAT_FREE}/g"` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF_DIR/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -L${NETCDFF_DIR}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb new file mode 100644 index 00000000000..64e92c7f014 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb @@ -0,0 +1,44 @@ +name = 'WRF' +version = '4.6.1' +buildtype = 'dmpar' +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.mmm.ucar.edu/models/wrf' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +github_account = 'wrf-model' +source_urls = [GITHUB_RELEASE] +sources = ['v%(version)s.tar.gz'] +patches = ['WRF-4.6.1_netCDF-Fortran_separate_path.patch'] + +checksums = [ + {'v4.6.1.tar.gz': 'b8ec11b240a3cf1274b2bd609700191c6ec84628e4c991d3ab562ce9dc50b5f2'}, + {'WRF-4.6.1_netCDF-Fortran_separate_path.patch': + '0fcc55df295910fe507a3938b420a9a211e6e2ce82de8ded347b54135994e716'}, +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20231222'), + ('tcsh', '6.24.13'), + ('time', '1.9'), + ('Perl', '5.38.2'), +] + +dependencies = [ + ('JasPer', '4.2.4'), + ('netCDF', '4.9.2'), + ('netCDF-Fortran', '4.6.1'), +] + +runtest = True + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch new file mode 100644 index 00000000000..b2f654ab876 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch @@ -0,0 +1,156 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain +# +# updated for WPS v4.4 by Maxim Masterov (SURF) +# updated for WRF v4.5.1 by Stefan Wolfsheimer (SURF) +# updated for WRF v4.6.1 by Stefan Wolfsheimer (SURF) + + +diff -Nru WRFV4.6.1.orig/arch/Config.pl WRFV4.6.1/arch/Config.pl +--- WRFV4.6.1.orig/arch/Config.pl 2024-10-16 23:05:18.000000000 +0200 ++++ WRFV4.6.1/arch/Config.pl 2024-11-28 15:38:43.864070000 +0100 +@@ -11,6 +11,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; + $sw_pnetcdf_path = "" ; + $sw_netcdfpar_path = "" ; + $sw_adios2_path = "" ; +@@ -70,6 +71,10 @@ + { + $sw_netcdf_path = substr( $ARGV[0], 8 ) ; + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 16 ) eq "netcdf4_dep_lib=" ) + { + $sw_netcdf4_dep_lib = substr( $ARGV[0], 17 ) ; +@@ -626,6 +631,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_NETCDFPAR_PATH/$sw_netcdfpar_path/g ; + $_ =~ s/CONFIGURE_ADIOS2_PATH/$sw_adios2_path/g ; +@@ -695,7 +701,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdff_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +@@ -1083,7 +1089,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdff_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -Nru WRFV4.6.1.orig/arch/postamble WRFV4.6.1/arch/postamble +--- WRFV4.6.1.orig/arch/postamble 2024-10-16 23:05:18.000000000 +0200 ++++ WRFV4.6.1/arch/postamble 2024-11-28 15:38:38.086016000 +0100 +@@ -55,7 +55,8 @@ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ + -I$(NETCDFPATH)/include \ +- CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC ++ -I$(NETCDFFPATH)/include \ ++ CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC + REGISTRY = Registry + CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE + +@@ -64,6 +65,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -96,7 +98,7 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" NETCDF4_DEP_LIB="$(NETCDF4_DEP_LIB)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + +diff -Nru WRFV4.6.1.orig/configure WRFV4.6.1/configure +--- WRFV4.6.1.orig/configure 2024-11-28 15:36:44.834084000 +0100 ++++ WRFV4.6.1/configure 2024-11-28 15:51:45.766140000 +0100 +@@ -242,10 +242,13 @@ + USENETCDFF="" + USENETCDF="" + if [ -n "$NETCDF" ] ; then +- echo "Will use NETCDF in dir: $NETCDF" ++ echo "Will use NETCDF in dir: $NETCDF" ++ echo "Will use NETCDFF in dir: $NETCDFF" + # Oh UNIDATA, why make it so hard ... + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then + USENETCDFF="-lnetcdff" ++ elif [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib/libnetcdff.dll.a" ] ; then ++ USENETCDFF="-lnetcdff" + else + USENETCDFF=" " + fi +@@ -265,7 +268,6 @@ + echo ' ' + exit 6 + fi +- + # If the user asked for classic netcdf, acquiesce to the request. + + if [ ! -f "$NETCDF/bin/nf-config" ] ; then +@@ -538,7 +540,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -netcdf4_dep_lib="$NETCDF4_DEP_LIB" +@@ -620,14 +622,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo + echo "Error : Not found $NETCDF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -Nru WRFV4.6.1.orig/external/io_netcdf/makefile WRFV4.6.1/external/io_netcdf/makefile +--- WRFV4.6.1.orig/external/io_netcdf/makefile 2024-10-16 23:05:19.000000000 +0200 ++++ WRFV4.6.1/external/io_netcdf/makefile 2024-11-28 16:38:31.349880802 +0100 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share ++FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include -I../ioapi_share + LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar From 420e7e805f11787e63923515cd08cc57b7a3e37e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 10:23:43 +0100 Subject: [PATCH 08/34] added JasPer patch --- .../w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb | 2 + .../w/WPS/WPS-4.6.0_fix_jasper_decode.patch | 122 ++++++++++++++++++ 2 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb index 45612b84fa5..ddf1835f790 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb @@ -13,10 +13,12 @@ source_urls = ['https://github.com/wrf-model/WPS/archive/'] sources = ['v%(version)s.tar.gz'] patches = [ 'WPS-%(version)s_netCDF-Fortran_separate_path.patch', + 'WPS-4.6.0_fix_jasper_decode.patch', ] checksums = [ 'ca7bbfc6c28a107c6eb00ded70e693f5c9a3926ecde7656f49e306c9eb9a309b', # v4.6.1.tar.gz 'ed49d5af4e6c80d9ddd9954b968c514cf888c3b35dce64744d1ac1eaa38b7042', # WPS-4.4_netCDF-Fortran_separate_path.patch + '60bc9feae34a5939cc749582554712c0370606b06c6cd49235260137475c7c8e', # WPS-4.6.0_fix_jasper_decode.patch ] buildtype = "dmpar" diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch new file mode 100644 index 00000000000..7d1f3c49e28 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch @@ -0,0 +1,122 @@ +# Using correct JasPer functions +# ============================== +# WPS uses depreceated version of JasPer interface. +# See https://github.com/wrf-model/WPS/issues/207 +# @author Stefan Wolfsheimer (SURF) + + +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/base/jas_init.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/base/jas_init.c +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/base/jas_init.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/base/jas_init.c 2024-11-29 10:17:24.964788000 +0100 +@@ -123,8 +123,8 @@ + jas_image_addfmt(fmtid, "jp2", "jp2", + "JPEG-2000 JP2 File Format Syntax (ISO/IEC 15444-1)", &fmtops); + ++fmtid; +- fmtops.decode = jpc_decode; +- fmtops.encode = jpc_encode; ++ fmtops.decode = jas_image_decode; ++ fmtops.encode = jas_image_encode; + fmtops.validate = jpc_validate; + jas_image_addfmt(fmtid, "jpc", "jpc", + "JPEG-2000 Code Stream Syntax (ISO/IEC 15444-1)", &fmtops); +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h WPS-4.6.0/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h 2024-11-29 10:17:24.977624441 +0100 +@@ -557,8 +557,8 @@ + + #if !defined(EXCLUDE_JPC_SUPPORT) + /* Format-dependent operations for JPEG-2000 code stream support. */ +-jas_image_t *jpc_decode(jas_stream_t *in, const char *optstr); +-int jpc_encode(jas_image_t *image, jas_stream_t *out, const char *optstr); ++jas_image_t *jas_image_decode(jas_stream_t *in, const char *optstr); ++int jas_image_encode(jas_image_t *image, jas_stream_t *out, const char *optstr); + int jpc_validate(jas_stream_t *in); + #endif + +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c 2024-11-29 10:17:24.990192019 +0100 +@@ -215,7 +215,7 @@ + goto error; + } + +- if (!(dec->image = jpc_decode(in, optstr))) { ++ if (!(dec->image = jas_image_decode(in, optstr))) { + jas_eprintf("error: cannot decode code stream\n"); + goto error; + } +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c 2024-11-29 10:17:25.002777520 +0100 +@@ -346,7 +346,7 @@ + sprintf(buf, "%s\n_jp2overhead=%lu\n", (optstr ? optstr : ""), + (unsigned long) overhead); + +- if (jpc_encode(image, out, buf)) { ++ if (jas_image_encode(image, out, buf)) { + goto error; + } + +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c 2024-11-29 10:17:25.015484538 +0100 +@@ -235,7 +235,7 @@ + * The main entry point for the JPEG-2000 decoder. + \******************************************************************************/ + +-jas_image_t *jpc_decode(jas_stream_t *in, const char *optstr) ++jas_image_t *jas_image_decode(jas_stream_t *in, const char *optstr) + { + jpc_dec_importopts_t *opts; + jpc_dec_t *dec; +@@ -244,7 +244,7 @@ + dec = 0; + opts = 0; + +- JAS_DBGLOG(100, ("jpc_decode(%p, \"%s\")\n", in, optstr)); ++ JAS_DBGLOG(100, ("jas_image_decode(%p, \"%s\")\n", in, optstr)); + + if (!(opts = jpc_dec_opts_create(optstr))) { + goto error; +diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c +--- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c 2024-11-29 10:17:25.028597372 +0100 +@@ -277,7 +277,7 @@ + * The main encoder entry point. + \******************************************************************************/ + +-int jpc_encode(jas_image_t *image, jas_stream_t *out, const char *optstr) ++int jas_image_encode(jas_image_t *image, jas_stream_t *out, const char *optstr) + { + jpc_enc_t *enc; + jpc_enc_cp_t *cp; +diff -Nru WPS-4.6.0.orig/ungrib/src/ngl/g2/dec_jpeg2000.c WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c +--- WPS-4.6.0.orig/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-11-29 10:17:25.041671000 +0100 +@@ -80,9 +80,9 @@ + /* + * Decode JPEG200 codestream into jas_image_t structure. + */ +- image=jpc_decode(jpcstream,opts); ++ image=jas_image_decode(jpcstream,opts); + if ( image == 0 ) { +- printf(" jpc_decode return = %d \n",ier); ++ printf(" jas_image_decode return = %d \n",ier); + return -3; + } + +diff -Nru WPS-4.6.0.orig/ungrib/src/ngl/g2/enc_jpeg2000.c WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c +--- WPS-4.6.0.orig/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-06-13 00:06:55.000000000 +0200 ++++ WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-11-29 10:17:25.054123000 +0100 +@@ -178,9 +178,9 @@ + /* + * Encode image. + */ +- ier=jpc_encode(&image,jpcstream,opts); ++ ier=jas_image_encode(&image,jpcstream,opts); + if ( ier != 0 ) { +- printf(" jpc_encode return = %d \n",ier); ++ printf(" jas_image_encode return = %d \n",ier); + return -3; + } + /* From c28eafd236ff55e96a2794cfd7592878041aeb3e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 11:10:30 +0100 Subject: [PATCH 09/34] fix patch --- .../w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb | 3 +- .../w/WPS/WPS-4.6.0_fix_jasper_decode.patch | 105 ++---------------- 2 files changed, 9 insertions(+), 99 deletions(-) diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb index ddf1835f790..389aac870e5 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0-foss-2024a-dmpar.eb @@ -15,10 +15,11 @@ patches = [ 'WPS-%(version)s_netCDF-Fortran_separate_path.patch', 'WPS-4.6.0_fix_jasper_decode.patch', ] + checksums = [ 'ca7bbfc6c28a107c6eb00ded70e693f5c9a3926ecde7656f49e306c9eb9a309b', # v4.6.1.tar.gz 'ed49d5af4e6c80d9ddd9954b968c514cf888c3b35dce64744d1ac1eaa38b7042', # WPS-4.4_netCDF-Fortran_separate_path.patch - '60bc9feae34a5939cc749582554712c0370606b06c6cd49235260137475c7c8e', # WPS-4.6.0_fix_jasper_decode.patch + 'f4ea3c77c42c3474d582e311b8bd0d80c67243f45922e85ee3ff52df61d6c77e', # WPS-4.6.0_fix_jasper_decode.patch ] buildtype = "dmpar" diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch index 7d1f3c49e28..4f6d416931f 100644 --- a/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch +++ b/easybuild/easyconfigs/w/WPS/WPS-4.6.0_fix_jasper_decode.patch @@ -5,118 +5,27 @@ # @author Stefan Wolfsheimer (SURF) -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/base/jas_init.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/base/jas_init.c ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/base/jas_init.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/base/jas_init.c 2024-11-29 10:17:24.964788000 +0100 -@@ -123,8 +123,8 @@ - jas_image_addfmt(fmtid, "jp2", "jp2", - "JPEG-2000 JP2 File Format Syntax (ISO/IEC 15444-1)", &fmtops); - ++fmtid; -- fmtops.decode = jpc_decode; -- fmtops.encode = jpc_encode; -+ fmtops.decode = jas_image_decode; -+ fmtops.encode = jas_image_encode; - fmtops.validate = jpc_validate; - jas_image_addfmt(fmtid, "jpc", "jpc", - "JPEG-2000 Code Stream Syntax (ISO/IEC 15444-1)", &fmtops); -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h WPS-4.6.0/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/include/jasper/jas_image.h 2024-11-29 10:17:24.977624441 +0100 -@@ -557,8 +557,8 @@ - - #if !defined(EXCLUDE_JPC_SUPPORT) - /* Format-dependent operations for JPEG-2000 code stream support. */ --jas_image_t *jpc_decode(jas_stream_t *in, const char *optstr); --int jpc_encode(jas_image_t *image, jas_stream_t *out, const char *optstr); -+jas_image_t *jas_image_decode(jas_stream_t *in, const char *optstr); -+int jas_image_encode(jas_image_t *image, jas_stream_t *out, const char *optstr); - int jpc_validate(jas_stream_t *in); - #endif - -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_dec.c 2024-11-29 10:17:24.990192019 +0100 -@@ -215,7 +215,7 @@ - goto error; - } - -- if (!(dec->image = jpc_decode(in, optstr))) { -+ if (!(dec->image = jas_image_decode(in, optstr))) { - jas_eprintf("error: cannot decode code stream\n"); - goto error; - } -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jp2/jp2_enc.c 2024-11-29 10:17:25.002777520 +0100 -@@ -346,7 +346,7 @@ - sprintf(buf, "%s\n_jp2overhead=%lu\n", (optstr ? optstr : ""), - (unsigned long) overhead); - -- if (jpc_encode(image, out, buf)) { -+ if (jas_image_encode(image, out, buf)) { - goto error; - } - -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_dec.c 2024-11-29 10:17:25.015484538 +0100 -@@ -235,7 +235,7 @@ - * The main entry point for the JPEG-2000 decoder. - \******************************************************************************/ - --jas_image_t *jpc_decode(jas_stream_t *in, const char *optstr) -+jas_image_t *jas_image_decode(jas_stream_t *in, const char *optstr) - { - jpc_dec_importopts_t *opts; - jpc_dec_t *dec; -@@ -244,7 +244,7 @@ - dec = 0; - opts = 0; - -- JAS_DBGLOG(100, ("jpc_decode(%p, \"%s\")\n", in, optstr)); -+ JAS_DBGLOG(100, ("jas_image_decode(%p, \"%s\")\n", in, optstr)); - - if (!(opts = jpc_dec_opts_create(optstr))) { - goto error; -diff -Nru WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c ---- WPS-4.6.0.orig/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/external/jasper-1.900.29/src/libjasper/jpc/jpc_enc.c 2024-11-29 10:17:25.028597372 +0100 -@@ -277,7 +277,7 @@ - * The main encoder entry point. - \******************************************************************************/ - --int jpc_encode(jas_image_t *image, jas_stream_t *out, const char *optstr) -+int jas_image_encode(jas_image_t *image, jas_stream_t *out, const char *optstr) - { - jpc_enc_t *enc; - jpc_enc_cp_t *cp; diff -Nru WPS-4.6.0.orig/ungrib/src/ngl/g2/dec_jpeg2000.c WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c --- WPS-4.6.0.orig/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-11-29 10:17:25.041671000 +0100 -@@ -80,9 +80,9 @@ ++++ WPS-4.6.0/ungrib/src/ngl/g2/dec_jpeg2000.c 2024-11-29 10:58:34.322941000 +0100 +@@ -80,7 +80,7 @@ /* * Decode JPEG200 codestream into jas_image_t structure. */ - image=jpc_decode(jpcstream,opts); -+ image=jas_image_decode(jpcstream,opts); ++ image=jas_image_decode(jpcstream,jas_image_getfmt(jpcstream),opts); if ( image == 0 ) { -- printf(" jpc_decode return = %d \n",ier); -+ printf(" jas_image_decode return = %d \n",ier); + printf(" jpc_decode return = %d \n",ier); return -3; - } - diff -Nru WPS-4.6.0.orig/ungrib/src/ngl/g2/enc_jpeg2000.c WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c --- WPS-4.6.0.orig/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-06-13 00:06:55.000000000 +0200 -+++ WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-11-29 10:17:25.054123000 +0100 -@@ -178,9 +178,9 @@ ++++ WPS-4.6.0/ungrib/src/ngl/g2/enc_jpeg2000.c 2024-11-29 10:58:40.467583000 +0100 +@@ -178,7 +178,7 @@ /* * Encode image. */ - ier=jpc_encode(&image,jpcstream,opts); + ier=jas_image_encode(&image,jpcstream,opts); if ( ier != 0 ) { -- printf(" jpc_encode return = %d \n",ier); -+ printf(" jas_image_encode return = %d \n",ier); + printf(" jpc_encode return = %d \n",ier); return -3; - } - /* From e420a130cff12a566afbd2a5818d431d2eb68c64 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 17:27:00 +0100 Subject: [PATCH 10/34] removed patch --- .../w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb | 9 +- ...F-4.6.1_netCDF-Fortran_separate_path.patch | 156 ------------------ 2 files changed, 6 insertions(+), 159 deletions(-) delete mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb index 64e92c7f014..26865bf2a0e 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb @@ -14,12 +14,13 @@ toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 github_account = 'wrf-model' source_urls = [GITHUB_RELEASE] sources = ['v%(version)s.tar.gz'] -patches = ['WRF-4.6.1_netCDF-Fortran_separate_path.patch'] + +# patches = ['WRF-4.6.1_netCDF-Fortran_separate_path.patch'] checksums = [ {'v4.6.1.tar.gz': 'b8ec11b240a3cf1274b2bd609700191c6ec84628e4c991d3ab562ce9dc50b5f2'}, - {'WRF-4.6.1_netCDF-Fortran_separate_path.patch': - '0fcc55df295910fe507a3938b420a9a211e6e2ce82de8ded347b54135994e716'}, +# {'WRF-4.6.1_netCDF-Fortran_separate_path.patch': +# '0fcc55df295910fe507a3938b420a9a211e6e2ce82de8ded347b54135994e716'}, ] # csh is used by WRF install scripts @@ -36,6 +37,8 @@ dependencies = [ ('netCDF-Fortran', '4.6.1'), ] +preconfigopts = "export NETCDF=$EBROOTNETCDFMINFORTRAN && export NETCDF_C=$EBROOTNETCDF &&" + runtest = True # limit parallel build to 20 diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch deleted file mode 100644 index b2f654ab876..00000000000 --- a/easybuild/easyconfigs/w/WRF/WRF-4.6.1_netCDF-Fortran_separate_path.patch +++ /dev/null @@ -1,156 +0,0 @@ -# Allow netCDF library with separate directories for C and Fortran -# ============================================================================ -# This patch has been around in EasyBuild since WRF3.5; it was committed by -# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain -# -# updated for WPS v4.4 by Maxim Masterov (SURF) -# updated for WRF v4.5.1 by Stefan Wolfsheimer (SURF) -# updated for WRF v4.6.1 by Stefan Wolfsheimer (SURF) - - -diff -Nru WRFV4.6.1.orig/arch/Config.pl WRFV4.6.1/arch/Config.pl ---- WRFV4.6.1.orig/arch/Config.pl 2024-10-16 23:05:18.000000000 +0200 -+++ WRFV4.6.1/arch/Config.pl 2024-11-28 15:38:43.864070000 +0100 -@@ -11,6 +11,7 @@ - select((select(STDOUT), $|=1)[0]); - $sw_perl_path = perl ; - $sw_netcdf_path = "" ; -+$sw_netcdff_path = "" ; - $sw_pnetcdf_path = "" ; - $sw_netcdfpar_path = "" ; - $sw_adios2_path = "" ; -@@ -70,6 +71,10 @@ - { - $sw_netcdf_path = substr( $ARGV[0], 8 ) ; - } -+ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) -+ { -+ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; -+ } - if ( substr( $ARGV[0], 1, 16 ) eq "netcdf4_dep_lib=" ) - { - $sw_netcdf4_dep_lib = substr( $ARGV[0], 17 ) ; -@@ -626,6 +631,7 @@ - { - $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; - $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; -+ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; - $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; - $_ =~ s/CONFIGURE_NETCDFPAR_PATH/$sw_netcdfpar_path/g ; - $_ =~ s/CONFIGURE_ADIOS2_PATH/$sw_adios2_path/g ; -@@ -695,7 +701,7 @@ - } elsif ( $sw_os eq "Interix" ) { - $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; - } else { -- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; -+ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdff_path/lib $sw_usenetcdff $sw_usenetcdf : ; - } - } - else -@@ -1083,7 +1089,7 @@ - } elsif ( $sw_os eq "Interix" ) { - $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; - } else { -- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; -+ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib -L$sw_netcdff_path/lib $sw_usenetcdff $sw_usenetcdf : ; - } - } - else -diff -Nru WRFV4.6.1.orig/arch/postamble WRFV4.6.1/arch/postamble ---- WRFV4.6.1.orig/arch/postamble 2024-10-16 23:05:18.000000000 +0200 -+++ WRFV4.6.1/arch/postamble 2024-11-28 15:38:38.086016000 +0100 -@@ -55,7 +55,8 @@ - -I$(WRF_SRC_ROOT_DIR)/wrftladj \ - -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ - -I$(NETCDFPATH)/include \ -- CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC -+ -I$(NETCDFFPATH)/include \ -+ CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC - REGISTRY = Registry - CC_TOOLS_CFLAGS = CONFIGURE_NMM_CORE - -@@ -64,6 +65,7 @@ - ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS - CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE - NETCDFPATH = CONFIGURE_NETCDF_PATH -+NETCDFFPATH = CONFIGURE_NETCDFF_PATH - HDF5PATH = CONFIGURE_HDF5_PATH - WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH - RTTOVPATH = CONFIGURE_RTTOV_PATH -@@ -96,7 +98,7 @@ - - wrfio_nf : - ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ -- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ -+ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ - CC="$(SCC)" CFLAGS="$(CFLAGS)" NETCDF4_DEP_LIB="$(NETCDF4_DEP_LIB)" \ - FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) - -diff -Nru WRFV4.6.1.orig/configure WRFV4.6.1/configure ---- WRFV4.6.1.orig/configure 2024-11-28 15:36:44.834084000 +0100 -+++ WRFV4.6.1/configure 2024-11-28 15:51:45.766140000 +0100 -@@ -242,10 +242,13 @@ - USENETCDFF="" - USENETCDF="" - if [ -n "$NETCDF" ] ; then -- echo "Will use NETCDF in dir: $NETCDF" -+ echo "Will use NETCDF in dir: $NETCDF" -+ echo "Will use NETCDFF in dir: $NETCDFF" - # Oh UNIDATA, why make it so hard ... - if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then - USENETCDFF="-lnetcdff" -+ elif [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib/libnetcdff.dll.a" ] ; then -+ USENETCDFF="-lnetcdff" - else - USENETCDFF=" " - fi -@@ -265,7 +268,6 @@ - echo ' ' - exit 6 - fi -- - # If the user asked for classic netcdf, acquiesce to the request. - - if [ ! -f "$NETCDF/bin/nf-config" ] ; then -@@ -538,7 +540,7 @@ - srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` - if [ -n "$srch" ] ; then - $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ -- -netcdf=$NETCDF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ -+ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -adios2=$ADIOS2 -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ - -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ - -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ - -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -netcdf4_dep_lib="$NETCDF4_DEP_LIB" -@@ -620,14 +622,14 @@ - echo "If you wish to change the default options, edit the file:" - echo " arch/configure.defaults" - --if test -n "$NETCDF" ; then -- if [ ! -f $NETCDF/include/netcdf.inc ] ; then -+if test -n "$NETCDFF" ; then -+ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then - echo - echo "Error : Not found $NETCDF/include/netcdf.inc" - echo " Please check this installation of NetCDF and re-run this configure script" - exit -1 - fi -- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null -+ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null - configure_aaaa=$? ; export configure_aaaa - if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then - echo "NetCDF users note:" -diff -Nru WRFV4.6.1.orig/external/io_netcdf/makefile WRFV4.6.1/external/io_netcdf/makefile ---- WRFV4.6.1.orig/external/io_netcdf/makefile 2024-10-16 23:05:19.000000000 +0200 -+++ WRFV4.6.1/external/io_netcdf/makefile 2024-11-28 16:38:31.349880802 +0100 -@@ -3,9 +3,9 @@ - OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o - OBJS = $(OBJSL) - CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code --FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share -+FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include -I../ioapi_share - LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf --LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) -+LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) - CPP1 = $(CPP) -P $(TRADFLAG) - M4 = m4 -Uinclude -Uindex -Ulen - AR = ar From dc96e2dfa9a3b8faeea2081e3decbb71d9110cfe Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 29 Nov 2024 17:31:54 +0100 Subject: [PATCH 11/34] removed commented lines --- easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb index 26865bf2a0e..82904273536 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.6.1-foss-2024a-dmpar.eb @@ -15,12 +15,10 @@ github_account = 'wrf-model' source_urls = [GITHUB_RELEASE] sources = ['v%(version)s.tar.gz'] -# patches = ['WRF-4.6.1_netCDF-Fortran_separate_path.patch'] +# WRF-4.5.1_netCDF-Fortran_separate_path.patch no longer required for version 4.5.2 checksums = [ {'v4.6.1.tar.gz': 'b8ec11b240a3cf1274b2bd609700191c6ec84628e4c991d3ab562ce9dc50b5f2'}, -# {'WRF-4.6.1_netCDF-Fortran_separate_path.patch': -# '0fcc55df295910fe507a3938b420a9a211e6e2ce82de8ded347b54135994e716'}, ] # csh is used by WRF install scripts From 0bdc75d8bb9b0d4c5c426547ca0ddfd532870d75 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 3 Dec 2024 12:21:52 +0100 Subject: [PATCH 12/34] adding easyconfigs: BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb --- .../BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..c8ea0187e5a --- /dev/null +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,91 @@ +easyblock = 'Tarball' + +name = 'BindCraft' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/martinpacesa/BindCraft' +description = """Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. + Select your target and let the script do the rest of the work and finish once you have enough designs to order!""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Seaborn', '0.13.2'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0', versionsuffix), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('PyRosetta', '4.release-387'), + ('jax', '0.4.25', versionsuffix), + ('dm-haiku', '0.0.12', versionsuffix), + ('dm-tree', '0.1.8'), + ('ml-collections', '0.1.1'), + ('Optax', '0.2.2', versionsuffix), + ('py3Dmol', '2.1.0'), + ('JupyterLab', '4.0.5'), + ('hatchling', '1.18.0'), + ('Flax', '0.8.4', versionsuffix), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + # older version compatible with `jupyterlab-4.0.5` + ('notebook', '7.0.8', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['7f421b3fd46a17d91830e724b94e8e9ae922af152ebfd48b1e13ae4a07d8193c'], + }), + ('jupyter', '1.1.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['7a59533c22af65439b24bbe60373a4e95af8f16ac65a6c00820ad378e3f7cc83'], + }), + ('immutabledict', '4.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d728b2c2410d698d95e6200237feb50a695584d20289ad3379a439aa3d90baba'], + }), + ('colabdesign', '1.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8f556fb575d2bbef79fa1789698d55221f2cc51df38f2cc054f38cb6ecc08e27'], + }), +] + +fix_python_shebang_for = ['bindcraft.py'] + +postinstallcmds = ['chmod a+x %(installdir)s/bindcraft.py'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': ['bindcraft.py'], + 'dirs': [], +} + +sanity_check_commands = ["bindcraft.py --help"] + +moduleclass = 'bio' From 17174c2e66a17bc50c16a439831fc4b999d2f985 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 3 Dec 2024 14:36:56 +0100 Subject: [PATCH 13/34] adding easyconfigs: GPAW-setups-24.11.0.eb --- .../g/GPAW-setups/GPAW-setups-24.11.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb diff --git a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb new file mode 100644 index 00000000000..7edbb913770 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.11.0.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'GPAW-setups' +version = '24.11.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """PAW setups for the GPAW Density Functional Theory package. +Users can install setups manually using 'gpaw install-data' or use setups from this package. +The versions of GPAW and GPAW-setups can be intermixed. + +Compared to version 0.9.20000, version 24.1.0 contains an new improved Cr setup with 14 electrons, +which can be manually selected. Otherwise no changes are made, so no results will change. + +Version 21.11.0 contains setups for the Lanthanides. +""" + +toolchain = SYSTEM +source_urls = ['https://wiki.fysik.dtu.dk/gpaw-files/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['964c81cc28f7f91a4686d3d3182c4ebda30efb09d3f96b7f95eae3146499c110'] + +modextrapaths = {'GPAW_SETUP_PATH': ''} + +moduleclass = 'chem' + +sanity_check_paths = { + 'files': ['H.LDA.gz'], + 'dirs': [] +} From 250ae54bb87d35a9228c8d689a966ec3b6251299 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Fri, 6 Dec 2024 13:06:09 +0100 Subject: [PATCH 14/34] adding easyconfigs: Gurobi-12.0.0-GCCcore-13.2.0.eb --- .../g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..48f991538d9 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,64 @@ +name = 'Gurobi' +version = '12.0.0' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +local_archs = {'aarch64': 'armlinux64', 'x86_64': 'linux64'} +sources = ['gurobi%%(version)s_%s.tar.gz' % local_archs[ARCH]] +patches = ['Gurobi-11.0.0_use-eb-python-gurobi-shell.patch'] +checksums = [ + {'gurobi12.0.0_linux64.tar.gz': 'a2bdc9c1d6bf8eb4e551a184af1ce8d7b0435ea8e7d19a017cc7d53fd5efda12', + 'gurobi12.0.0_armlinux64.tar.gz': '8e1202cbf0866a16fa78c3e4be0fa32888ec912f8ddf333c29561d057964ef86'}, + {'Gurobi-11.0.0_use-eb-python-gurobi-shell.patch': + '566473a3ba4e35b0e74595368f9f4133fc4a3c97cca84154c4b938645786e663'}, +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('gurobipy', version, { + 'sources': ['gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_%(arch)s.whl'], + 'checksums': [{ + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_aarch64.whl': + 'fc3892e3d88d0f8a01da75f12f74023d398ef599a9e1add66ed76313733e30fb', + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl': + 'a08fb42a5e7cb02cdb993c1381c8b8c5a3baeedcadd56e7288d8458a57b81442', + }], + }), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is mandatory for installation +# use EB_GUROBI_LICENSE_FILE environment variable, or +# uncomment and modify the following variable: +# license_file = '/path/to/my-license-file' +license_file = HOME + '/licenses/%(name)s.lic' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' From 7d19ea2bfbbd8d0a6c812a223544a25e6c4ff621 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 10 Dec 2024 15:52:09 +0100 Subject: [PATCH 15/34] add TorchRL to PyTorch-bundle v2.1.2 --- .../PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb | 10 ++++++++++ .../PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb | 10 ++++++++++ 2 files changed, 20 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb index d7e1c6cc2e0..985e8ad0158 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -179,6 +179,16 @@ exts_list = [ ), 'testinstall': True, }), + ('tensordict', '0.3.0', { + 'source_urls': ['https://github.com/pytorch/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f0d95e8f055c3f82838fdbeb03c6a907f8786c1046791db7e39cdcd9cb8f1889'], + }), + ('torchrl', '0.3.1', { + 'source_urls': ['https://github.com/pytorch/rl/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['882ed50cfd868c6b730834f2d7136a3039767061f075ba3cf194acf07e0be742'], + }), ] sanity_pip_check = True diff --git a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb index 4c8d8ef847a..50a7708dfa0 100644 --- a/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTorch-bundle/PyTorch-bundle-2.1.2-foss-2023a.eb @@ -176,6 +176,16 @@ exts_list = [ ), 'testinstall': True, }), + ('tensordict', '0.3.0', { + 'source_urls': ['https://github.com/pytorch/%(name)s/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f0d95e8f055c3f82838fdbeb03c6a907f8786c1046791db7e39cdcd9cb8f1889'], + }), + ('torchrl', '0.3.1', { + 'source_urls': ['https://github.com/pytorch/rl/archive'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['882ed50cfd868c6b730834f2d7136a3039767061f075ba3cf194acf07e0be742'], + }), ] sanity_pip_check = True From 9884b710c0455b055d9841545a33a860baf59c26 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 12 Dec 2024 14:51:21 +0100 Subject: [PATCH 16/34] adding easyconfigs: MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb, IDBA-UD-1.1.3-GCCcore-12.3.0.eb --- .../i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb | 51 +++++++++++++++++ ...toFinder-1.4.2-foss-2023a-Python-2.7.18.eb | 55 +++++++++++++++++++ 2 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..83d24a82eec --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCCcore-12.3.0.eb @@ -0,0 +1,51 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Updated: Pavel Grochal (INUITS) +# License: GPLv2 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in prebuildopts + +# modified by Tom Strempel +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.3' + +homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads +Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. +IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth +contigs are removed iteratively with cutoff threshold from low to high to reduce the errors +in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled +locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD +can iterate k value of de Bruijn graph to a very large value with less gaps and less branches +to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] +sources = ['idba-%(version)s.tar.gz'] +checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] + +builddependencies = [('binutils', '2.40')] + +prebuildopts = './configure && ' + +# we delete every .o and Makefile file which is left in bin folder +buildopts = ' && rm -fr bin/*.o bin/Makefile*' + +files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] + +pretestopts = "cd test && " +runtest = "check" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb b/easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb new file mode 100644 index 00000000000..b0262f35599 --- /dev/null +++ b/easybuild/easyconfigs/m/MitoFinder/MitoFinder-1.4.2-foss-2023a-Python-2.7.18.eb @@ -0,0 +1,55 @@ +easyblock = 'Tarball' + +name = 'MitoFinder' +version = '1.4.2' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/RemiAllio/MitoFinder' +description = """MitoFinder is a pipeline to assemble mitochondrial genomes and +annotate mitochondrial genes from trimmed read sequencing data""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/RemiAllio/MitoFinder/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2d6d3925fb014777df97f272134143cc518944ae05d000a44ada2862d46ec95a'] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('Python', '2.7.18'), + ('IDBA-UD', '1.1.3'), + ('Infernal', '1.1.5'), + ('tRNAscan-SE', '2.0.12'), + ('Automake', '1.16.5'), +] + +postinstallcmds = [ + # avoid run install.sh + link EB modules + "rm -rf %(installdir)s/idba/bin && cd %(installdir)s/idba && ln -s $EBROOTIDBAMINUD/bin && " + "cd %(installdir)s/metaspades/bin && ln -s spades.py metaspades.py && " + "cd %(installdir)s/trnascanSE && mkdir -p infernal-1.1.3/exec && cd infernal-1.1.3/exec && " + "ln -s $EBROOTINFERNAL/bin && ln -s $EBROOTINFERNAL/share && " + "cd %(installdir)s/trnascanSE && mkdir -p automake-1.13.4/exec && cd automake-1.13.4/exec && " + "ln -s $EBROOTAUTOMAKE/bin && ln -s $EBROOTAUTOMAKE/share && " + "cd %(installdir)s/trnascanSE && mkdir -p tRNAscan-SE-2.0/exec && cd tRNAscan-SE-2.0/exec && " + "ln -s $EBROOTTRNASCANMINSE/bin && ln -s $EBROOTTRNASCANMINSE/lib && ln -s $EBROOTTRNASCANMINSE/include && " + "cd %(installdir)s/mitfi && mkdir -p infernal-1.0.2/exec && cd infernal-1.0.2/exec && " + "ln -s $EBROOTINFERNAL/bin && ln -s $EBROOTINFERNAL/share && " + "cd %(installdir)s/mitfi/infernal-1.0.2 && ln -s $EBROOTINFERNAL/bin src && " + 'cd %(installdir)s && touch install.sh.ok && ' + # fix mitofinder - https://github.com/RemiAllio/MitoFinder/issues/26 + "sed -i 's/os.devnull, \'wb\')/os.devnull, \'wb\'), shell=True/g' mitofinder" +] + +fix_python_shebang_for = ['mitofinder', '*.py'] + +sanity_check_paths = { + 'files': ['mitofinder'], + 'dirs': ['idba', 'megahit', 'metaspades', 'mitfi', 'trnascanSE'], +} + +sanity_check_commands = ['mitofinder -h'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From a8cae9bcaf1150ae78d991eefd83bc57061ea8fb Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 12 Dec 2024 16:28:29 +0000 Subject: [PATCH 17/34] update homepage for DFTB+ --- easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb | 4 +--- easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb | 6 +----- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb index 5711e31168d..dd4cc9c4f69 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'DFTB+' version = '21.1' -homepage = 'https://www.dftb-plus.info' +homepage = 'https://www.dftbplus.org/' description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB @@ -77,6 +77,4 @@ sanity_check_paths = { sanity_check_commands = [("python -c 'import dptools'")] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb index c862fcea552..bc04511e7da 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'DFTB+' version = '24.1' -homepage = 'https://www.dftb-plus.info' +homepage = 'https://www.dftbplus.org/' description = """DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB @@ -66,8 +66,6 @@ runtest = 'test' exts_defaultclass = 'PythonPackage' exts_default_options = { - 'download_dep_fail': True, - 'use_pip': True, 'runtest': False, } exts_list = [ @@ -88,6 +86,4 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import dptools'"] -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - moduleclass = 'phys' From abaf168d58121d617a07dda15ad7b6d6528a235f Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 12 Dec 2024 16:45:08 +0000 Subject: [PATCH 18/34] use EB4 as a starting point --- easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb | 2 ++ easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb | 4 ++++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb index dd4cc9c4f69..567ceb13c55 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-21.1-intel-2021a.eb @@ -77,4 +77,6 @@ sanity_check_paths = { sanity_check_commands = [("python -c 'import dptools'")] +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'phys' diff --git a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb index bc04511e7da..1d2538ed7d2 100644 --- a/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb +++ b/easybuild/easyconfigs/d/DFTB+/DFTB+-24.1-foss-2023a.eb @@ -66,6 +66,8 @@ runtest = 'test' exts_defaultclass = 'PythonPackage' exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, 'runtest': False, } exts_list = [ @@ -86,4 +88,6 @@ sanity_check_paths = { sanity_check_commands = ["python -c 'import dptools'"] +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + moduleclass = 'phys' From b37be0cb021aafaff34d44afd7b3be7136acf3fc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 13 Dec 2024 16:40:30 +0100 Subject: [PATCH 19/34] adding easyconfigs: ABRicate-1.0.0-gompi-2023b.eb, BLAST+-2.16.0-gompi-2023b.eb, BWA-0.7.18-GCCcore-13.2.0.eb, prokka-1.14.5-gompi-2023b.eb, SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb, VCFtools-0.1.16-GCC-13.2.0.eb --- .../a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb | 41 +++++++++++ .../any2fasta-0.4.2-GCCcore-13.2.0.eb | 35 ++++++++++ .../b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb | 58 ++++++++++++++++ .../b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb | 52 ++++++++++++++ .../Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb | 28 ++++++++ .../p/prokka/prokka-1.14.5-gompi-2023b.eb | 50 ++++++++++++++ .../SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb | 37 ++++++++++ .../tbl2asn-20230713-GCCcore-13.2.0.eb | 69 +++++++++++++++++++ .../v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb | 36 ++++++++++ 9 files changed, 406 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb new file mode 100644 index 00000000000..3e980962ec8 --- /dev/null +++ b/easybuild/easyconfigs/a/ABRicate/ABRicate-1.0.0-gompi-2023b.eb @@ -0,0 +1,41 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'ABRicate' +version = '1.0.0' + +homepage = 'https://github.com/tseemann/abricate' +description = "Mass screening of contigs for antimicrobial and virulence genes" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +# https://github.com/tseemann/abricate +github_account = 'tseemann' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['e7e2af45e47b887c4dba754af87a24014dcb5552eb3fe2a3fd66bb5359a0daf9'] + +dependencies = [ + ('Perl', '5.38.0'), + ('any2fasta', '0.4.2'), + ('BioPerl', '1.7.8'), + ('BLAST+', '2.16.0'), +] + +postinstallcmds = ['%(installdir)s/bin/abricate --setupdb'] + +sanity_check_paths = { + 'files': ['bin/abricate', 'bin/abricate-get_db'], + 'dirs': ['db'], +} + +sanity_check_commands = [ + "abricate --help", + "abricate --list", +] + +modloadmsg = "abricate databases are located in $EBROOTABRICATE/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..91034a25be8 --- /dev/null +++ b/easybuild/easyconfigs/a/any2fasta/any2fasta-0.4.2-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +# Author: Pavel Grochal (INUITS) +# Updated by: Denis Kristak (INUITS) +# License: GPLv2 + +easyblock = 'Tarball' + +name = 'any2fasta' +version = '0.4.2' + +homepage = 'https://github.com/tseemann/any2fasta' +description = "Convert various sequence formats to FASTA" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +# https://github.com/tseemann/any2fasta +github_account = 'tseemann' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.zip'] +checksums = ['3faa738ab409c7073afe3769e9d32dd5b28a2c12e72c2e4ac6f4e9946ee9a22f'] + +dependencies = [('Perl', '5.38.0')] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['any2fasta'], + 'dirs': [], +} + +sanity_check_commands = [ + 'any2fasta -h', + 'any2fasta -q %(builddir)s/%(name)s-%(version)s/test.fq', +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb new file mode 100644 index 00000000000..d43cb118efd --- /dev/null +++ b/easybuild/easyconfigs/b/BLAST+/BLAST+-2.16.0-gompi-2023b.eb @@ -0,0 +1,58 @@ +# # +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos , Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of +# the policy: https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# # + +easyblock = 'ConfigureMake' + +name = 'BLAST+' +version = '2.16.0' + +homepage = 'https://blast.ncbi.nlm.nih.gov/' +description = """Basic Local Alignment Search Tool, or BLAST, is an algorithm + for comparing primary biological sequence information, such as the amino-acid + sequences of different proteins or the nucleotides of DNA sequences.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/blast/executables/%(namelower)s/%(version)s/'] +sources = ['ncbi-blast-%(version)s+-src.tar.gz'] +checksums = ['17c93cf009721023e5aecf5753f9c6a255d157561638b91b3ad7276fd6950c2b'] + +builddependencies = [('cpio', '2.15')] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.5'), + ('PCRE', '8.45'), + ('Boost', '1.83.0'), + ('GMP', '6.3.0'), + ('libpng', '1.6.40'), + ('libjpeg-turbo', '3.0.1'), + ('LMDB', '0.9.31'), + ('SQLite', '3.43.1'), +] + +# remove line that prepends system paths to $PATH from configure script +preconfigopts = r'sed -i "s|^PATH=\(.*\)$|#PATH=\1 |" %(start_dir)s/src/build-system/configure && ' + +configopts = "--with-z=$EBROOTZLIB --with-bz2=$EBROOTBZIP2 " +configopts += "--with-pcre=$EBROOTPCRE --with-boost=$EBROOTBOOST " +configopts += "--with-gmp=$EBROOTGMP --with-png=$EBROOTLIBPNG " +configopts += "--with-jpeg=$EBROOTLIBJPEGMINTURBO --with-lmdb=$EBROOTLMDB" + +sanity_check_paths = { + 'files': ['bin/blastn', 'bin/blastp', 'bin/blastx'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..d65b73e57e9 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.18-GCCcore-13.2.0.eb @@ -0,0 +1,52 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +# +# 0.7.18 +# Erica Bianco (HPCNow!) +## + +name = 'BWA' +version = '0.7.18' + +homepage = 'http://bio-bwa.sourceforge.net/' +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['194788087f7b9a77c0114aa481b2ef21439f6abab72488c83917302e8d0e7870'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('zlib', '1.2.13'), + ('Perl', '5.38.0'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb new file mode 100644 index 00000000000..b26850e9d30 --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-SearchIO-hmmer/Bio-SearchIO-hmmer-1.7.3-GCC-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PerlModule' + +name = 'Bio-SearchIO-hmmer' +version = '1.7.3' + +homepage = 'https://metacpan.org/pod/Bio::SearchIO::hmmer3' +description = """Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible +with both version 2 and version 3 of the HMMER package from http://hmmer.org.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'] +sources = [SOURCE_TAR_GZ] +checksums = ['686152f8ce7c611d27ee35ac002ecc309f6270e289a482993796a23bb5388246'] + +dependencies = [ + ('Perl', '5.38.0'), + ('BioPerl', '1.7.8'), +] + +options = {'modulename': 'Bio::SearchIO::hmmer3'} + +sanity_check_paths = { + 'files': ['bin/bp_%s.pl' % x for x in ['hmmer_to_table', 'parse_hmmsearch']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb new file mode 100644 index 00000000000..bd7648a5418 --- /dev/null +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023b.eb @@ -0,0 +1,50 @@ +# EasyBuild easyconfig +# +# John Dey jfdey@fredhutch.org +# Fred Hutchenson Cancer Research Center +# +# Updated: Pavel Grochal (INUITS) + +easyblock = 'Tarball' + +name = 'prokka' +version = '1.14.5' + +homepage = 'https://www.vicbioinformatics.com/software.prokka.shtml' +description = "Prokka is a software tool for the rapid annotation of prokaryotic genomes." + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = ['https://github.com/tseemann/prokka/archive/'] +sources = ['v%(version)s.zip'] +checksums = ['0c13dd5621c352633565f5831c4e85ce2e1e400c2f17ba50800282ae121803ff'] + +dependencies = [ + ('BioPerl', '1.7.8'), + ('BLAST+', '2.16.0'), + ('Java', '11', '', SYSTEM), + ('Bio-SearchIO-hmmer', '1.7.3'), + ('parallel', '20240322'), + ('tbl2asn', '20230713'), +] + +local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', + 'prokka-biocyc_to_fasta_db', 'prokka-clusters_to_hmm', 'prokka-hamap_to_hmm', + 'prokka-uniprot_to_fasta_db', 'prokka-build_kingdom_dbs', 'prokka-genbank_to_fasta_db', + 'prokka-make_tarball'] + +postinstallcmds = ["%(installdir)s/bin/prokka --setupdb"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bin_files] + ['binaries/linux/aragorn', 'db/cm/Bacteria', 'doc/ToDoList.txt'], + 'dirs': ['bin', 'binaries', 'db', 'db/cm', 'db/genus', 'db/hmm', 'db/kingdom', 'doc'], +} + +sanity_check_commands = [ + "prokka --version", + "prokka --listdb", +] + +modloadmsg = "prokka scripts are located in $EBROOTPROKKA/bin; databases are located in $EBROOTPROKKA/db\n" + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb new file mode 100644 index 00000000000..5baecf1ad17 --- /dev/null +++ b/easybuild/easyconfigs/s/SKESA/SKESA-2.4.0-gompi-2023b_saute.1.3.0_2.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'SKESA' +version = '2.4.0' +versionsuffix = '_saute.1.3.0_2' + +homepage = 'https://github.com/ncbi/SKESA' +description = "SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs." + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/ncbi/SKESA/archive/'] +sources = ['skesa.%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['dc5ad60f963afb09d3f2a3bab8917e657bd93364f0deca6e6844ede44968e979'] + +dependencies = [ + ('Boost', '1.83.0'), + ('SRA-Toolkit', '3.1.1'), + ('ncbi-vdb', '3.1.1'), +] + +prebuildopts = "touch %(builddir)s/ngs.done && " + +buildopts = 'CC="$CXX" CFLAGS="$CXXFLAGS" ' +buildopts += "NGS_DIR=%(builddir)s BOOST_PATH=$EBROOTBOOST NGS_PATH=$EBROOTSRAMINTOOLKIT VDB_PATH=$EBROOTNCBIMINVDB" + +files_to_copy = [(['skesa'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/skesa'], + 'dirs': [], +} + +sanity_check_commands = ["skesa --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3571e61aac4 --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-GCCcore-13.2.0.eb @@ -0,0 +1,69 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('patchelf', '0.18.0'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +# libraries that are copied to installdir need to be patched to have an RPATH section +# when EasyBuild is configured to use RPATH linking (required to pass RPATH sanity check); + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.linux64.gz', + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = [ + "if %(rpath_enabled)s; then " + " patchelf --force-rpath --set-rpath %(installdir)s/lib %(installdir)s/bin/tbl2asn;" + "fi", + "chmod +x %(installdir)s/bin/tbl2asn", +] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb new file mode 100644 index 00000000000..3a4edc7bc1c --- /dev/null +++ b/easybuild/easyconfigs/v/VCFtools/VCFtools-0.1.16-GCC-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'VCFtools' +version = '0.1.16' + +homepage = 'https://vcftools.github.io' +description = """The aim of VCFtools is to provide + easily accessible methods for working with complex + genetic variation data in the form of VCF files.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = '%(namelower)s' +source_urls = [GITHUB_LOWER_RELEASE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dbfc774383c106b85043daa2c42568816aa6a7b4e6abc965eeea6c47dde914e3'] + +builddependencies = [ + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('Perl', '5.38.0'), + ('HTSlib', '1.19.1'), +] + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/vcf-sort', 'bin/vcf-stats'], + 'dirs': [], +} + +modextrapaths = {'PERL5LIB': 'lib/perl5/site_perl'} + +moduleclass = 'bio' From 9a8105fb588ce65d08d01ad6dbfb45e1f33fdb13 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 15 Dec 2024 17:32:44 +0100 Subject: [PATCH 20/34] adding easyconfigs: Whisper-20240930-foss-2023a-CUDA-12.1.1.eb --- ...Whisper-20240930-foss-2023a-CUDA-12.1.1.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..3cb03e7142a --- /dev/null +++ b/easybuild/easyconfigs/w/Whisper/Whisper-20240930-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'Whisper' +version = '20240930' +versionsuffix = '-CUDA-12.1.1' + +homepage = 'https://github.com/openai/whisper' +description = "Whisper is a general-purpose speech recognition model" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('numba', '0.58.1'), + ('PyTorch', '2.1.2', versionsuffix), + ('tiktoken', '0.7.0'), + ('Triton', '2.1.0', versionsuffix), + ('FFmpeg', '6.0'), +] + +use_pip = True + +exts_list = [ + ('openai-whisper', version, { + 'modulename': 'whisper', + 'checksums': ['b7178e9c1615576807a300024f4daa6353f7e1a815dac5e38c33f1ef055dd2d2'], + }), +] + +sanity_check_paths = { + 'files': ['bin/whisper'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["whisper --help"] + +sanity_pip_check = True + +moduleclass = 'ai' From 1887eddcbbc213d382da0221e3be4c2f02865ddd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 16 Dec 2024 13:26:29 +0100 Subject: [PATCH 21/34] make hatchling only a build dependency --- .../b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb index c8ea0187e5a..6cc5d76a73d 100644 --- a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a-CUDA-12.1.1.eb @@ -14,6 +14,10 @@ source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('Python', '3.11.3'), @@ -32,7 +36,6 @@ dependencies = [ ('Optax', '0.2.2', versionsuffix), ('py3Dmol', '2.1.0'), ('JupyterLab', '4.0.5'), - ('hatchling', '1.18.0'), ('Flax', '0.8.4', versionsuffix), ] From 46c83d99a5b2dc47bcc6c36ae8de8adefa580695 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 16 Dec 2024 16:28:23 +0100 Subject: [PATCH 22/34] adding easyconfigs: SMV-6.9.5-GCCcore-12.3.0.eb --- .../s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..b164481d03e --- /dev/null +++ b/easybuild/easyconfigs/s/SMV/SMV-6.9.5-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'SMV' # SmokeView +version = '6.9.5' + +homepage = 'https://github.com/firemodels/smv' +description = """Smokeview is a visualization program that displays output of FDS and CFAST simulations.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/firemodels/smv/archive/'] +sources = [SOURCE_TAR_GZ] +checksums = ['6c6203f6d6cd83c3525c7447ce4201c8df373d18d0c992d607ad232a77590ef7'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('binutils', '2.40'), +] +dependencies = [ + ('libgd', '2.3.3'), + ('freeglut', '3.4.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('json-c', '0.16'), + ('Doxygen', '1.9.7'), + ('glew', '2.2.0', '-osmesa'), +] + +configopts = '-DVERIFICATION_TESTS=ON' + +sanity_check_commands = [ + 'smokediff -h', + 'smokezip -h', + 'smvq -h', + 'smokeview -h 2>&1 | grep "Visualize"', +] + +sanity_check_paths = { + 'files': ['bin/smokeview', 'bin/smokediff', 'bin/smokezip', 'bin/smvq'], + 'dirs': [], +} + +moduleclass = 'vis' From 0e8239afb5922bfd20cc2b109cf5680aa04996c8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 17 Dec 2024 08:53:39 +0100 Subject: [PATCH 23/34] move `hatchling` from deps to build deps for `BindCraft` --- .../easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb index 49345e486d8..fd6186d58ec 100644 --- a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb @@ -13,6 +13,10 @@ source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), @@ -30,7 +34,6 @@ dependencies = [ ('Optax', '0.2.2'), ('py3Dmol', '2.1.0'), ('JupyterLab', '4.0.5'), - ('hatchling', '1.18.0'), ('Flax', '0.8.4'), ] From a3d73f02f85adcfa41c5705613fbd9ef5ca3ce22 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 17 Dec 2024 15:20:26 +0100 Subject: [PATCH 24/34] adding easyconfigs: IGV-2.19.1-Java-17.eb --- .../easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb diff --git a/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb b/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb new file mode 100644 index 00000000000..9a2bc1d7398 --- /dev/null +++ b/easybuild/easyconfigs/i/IGV/IGV-2.19.1-Java-17.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by Adam Huffman +# Big Data Institute, University of Oxford + +easyblock = 'Tarball' + +name = 'IGV' +version = '2.19.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/software/igv/' +description = """This package contains command line utilities for + preprocessing, computing feature count density (coverage), sorting, and + indexing data files.""" + +toolchain = SYSTEM + +source_urls = ['http://data.broadinstitute.org/igv/projects/downloads/%(version_major)s.%(version_minor)s'] +sources = ['%(name)s_%(version)s.zip'] +checksums = ['e7d7803cab4e12e84f5359a3d73915a45acc6d676151ca18e91fb2d39432b568'] + +dependencies = [('Java', '17', '', SYSTEM)] + +sanity_check_paths = { + 'files': ['%(namelower)s.sh', 'lib/%(namelower)s.jar'], + 'dirs': [], +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 8688a026a812f5d75c4d3b147a1ce317eae6049a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 17 Dec 2024 19:08:28 +0000 Subject: [PATCH 25/34] fix conflict of multiple tbl2asn --- .../p/prokka/prokka-1.14.5-gompi-2023a.eb | 2 +- .../t/tbl2asn/tbl2asn-20230713-linux64.eb | 56 ------------------- 2 files changed, 1 insertion(+), 57 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb diff --git a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb index 05fe75468f6..2e84effbc53 100644 --- a/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb +++ b/easybuild/easyconfigs/p/prokka/prokka-1.14.5-gompi-2023a.eb @@ -25,7 +25,7 @@ dependencies = [ ('Java', '11', '', SYSTEM), ('Bio-SearchIO-hmmer', '1.7.3'), ('parallel', '20230722'), - ('tbl2asn', '20230713', '-linux64', SYSTEM), + ('tbl2asn', '20230713'), ] local_bin_files = ['prokka', 'prokka-cdd_to_hmm', 'prokka-genpept_to_fasta_db', 'prokka-tigrfams_to_hmm', diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb deleted file mode 100644 index 71b750650ba..00000000000 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb +++ /dev/null @@ -1,56 +0,0 @@ -# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ -# Author: Pablo Escobar Lopez -# sciCORE - University of Basel -# SIB Swiss Institute of Bioinformatics -# revised by Ariel Lozano - -easyblock = 'Bundle' - -name = 'tbl2asn' -version = '20230713' -versionsuffix = '-linux64' - -homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' -description = """Tbl2asn is a command-line program that automates the creation of - sequence records for submission to GenBank""" - -toolchain = SYSTEM -builddependencies = [ - ('binutils', '2.35'), -] - -default_easyblock = 'CmdCp' - -# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, -# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 -# checksums. - -components = [ - ('libidn', '1.34', { - 'easyblock': 'ConfigureMake', - 'source_urls': [GNU_SOURCE], - 'sources': [SOURCELOWER_TAR_GZ], - 'start_dir': '%(namelower)s-%(version)s', - 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], - }), - (name, version, { - 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % - (version[:4] + '-' + version[4:6] + '-' + version[6:])], - 'sources': [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:], - 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], - 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], - 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], - 'files_to_copy': [(['tbl2asn'], 'bin')], - }), -] - -postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] - -sanity_check_paths = { - 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], - 'dirs': ['include'], -} - -sanity_check_commands = ['tbl2asn --help'] - -moduleclass = 'bio' From ac210a3ccbf8373d4396673dcec48b86363590c6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 17 Dec 2024 19:39:54 +0000 Subject: [PATCH 26/34] restore tbl2asn-20230713-linux64.eb as it is still needed for prokka-1.14.5-gompi-2022b.eb --- .../t/tbl2asn/tbl2asn-20230713-linux64.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb new file mode 100644 index 00000000000..71b750650ba --- /dev/null +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb @@ -0,0 +1,56 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# revised by Ariel Lozano + +easyblock = 'Bundle' + +name = 'tbl2asn' +version = '20230713' +versionsuffix = '-linux64' + +homepage = 'https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/' +description = """Tbl2asn is a command-line program that automates the creation of + sequence records for submission to GenBank""" + +toolchain = SYSTEM +builddependencies = [ + ('binutils', '2.35'), +] + +default_easyblock = 'CmdCp' + +# It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, +# reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 +# checksums. + +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:], + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), +] + +postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] + +sanity_check_paths = { + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ['tbl2asn --help'] + +moduleclass = 'bio' From 4aa063e64098001f8c66a7b455ef3d64fd700a27 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 18 Dec 2024 13:45:09 +0000 Subject: [PATCH 27/34] add rsvg dep to DjVuLibre --- .../easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb index 355a9996fbc..f4b0e614fd7 100644 --- a/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb @@ -25,6 +25,7 @@ builddependencies = [ dependencies = [ ('libjpeg-turbo', '2.1.5.1'), ('LibTIFF', '4.5.0'), + ('librsvg', '2.58.0'), ] _bins = ['bin/%s' % x for x in ['any2djvu', 'bzz', 'c44', 'cjb2', 'cpaldjvu', 'csepdjvu', 'ddjvu', 'djvm', 'djvmcvt', From b7b40a3b44acc839c0e945487fa5841b0a56c892 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 18 Dec 2024 13:49:21 +0000 Subject: [PATCH 28/34] add Doxygen build dep to libheif --- easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb | 1 + easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb | 1 + easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb | 1 + easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb | 1 + 4 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb index bb5cb6bf57c..7850c1ed564 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb @@ -14,6 +14,7 @@ checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] builddependencies = [ ('CMake', '3.20.1'), + ('Doxygen', '1.9.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb index cf871e99182..31a01b9b103 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb @@ -14,6 +14,7 @@ checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] builddependencies = [ ('CMake', '3.22.1'), + ('Doxygen', '1.9.1'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb index 9d966d5571b..9eb3548d709 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb @@ -16,6 +16,7 @@ checksums = ['7f97e4205c0bd9f9b8560536c8bd2e841d1c9a6d610401eb3eb87ed9cdfe78ea'] builddependencies = [ ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), ] dependencies = [ diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb index ee355100089..77784e13457 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb @@ -16,6 +16,7 @@ checksums = ['8390baf4913eda0a183e132cec62b875fb2ef507ced5ddddc98dfd2f17780aee'] builddependencies = [ ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), ] dependencies = [ From 3a7d593be38b6948b3d703ea58f47d11060bf2ce Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 18 Dec 2024 15:12:13 +0000 Subject: [PATCH 29/34] edit libheif and libde265 to GCCcore --- ....11-GCC-11.3.0.eb => libde265-1.0.11-GCCcore-11.3.0.eb} | 3 ++- ....15-GCC-12.3.0.eb => libde265-1.0.15-GCCcore-12.3.0.eb} | 3 ++- ....0.8-GCC-11.2.0.eb => libde265-1.0.8-GCCcore-10.3.0.eb} | 7 +++++-- ....0.8-GCC-10.3.0.eb => libde265-1.0.8-GCCcore-11.2.0.eb} | 7 +++++-- ...12.0-GCC-10.3.0.eb => libheif-1.12.0-GCCcore-10.3.0.eb} | 3 ++- ...12.0-GCC-11.2.0.eb => libheif-1.12.0-GCCcore-11.2.0.eb} | 3 ++- ...16.2-GCC-11.3.0.eb => libheif-1.16.2-GCCcore-11.3.0.eb} | 3 ++- ...17.6-GCC-12.3.0.eb => libheif-1.17.6-GCCcore-12.3.0.eb} | 3 ++- 8 files changed, 22 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/l/libde265/{libde265-1.0.11-GCC-11.3.0.eb => libde265-1.0.11-GCCcore-11.3.0.eb} (91%) rename easybuild/easyconfigs/l/libde265/{libde265-1.0.15-GCC-12.3.0.eb => libde265-1.0.15-GCCcore-12.3.0.eb} (91%) rename easybuild/easyconfigs/l/libde265/{libde265-1.0.8-GCC-11.2.0.eb => libde265-1.0.8-GCCcore-10.3.0.eb} (83%) rename easybuild/easyconfigs/l/libde265/{libde265-1.0.8-GCC-10.3.0.eb => libde265-1.0.8-GCCcore-11.2.0.eb} (83%) rename easybuild/easyconfigs/l/libheif/{libheif-1.12.0-GCC-10.3.0.eb => libheif-1.12.0-GCCcore-10.3.0.eb} (92%) rename easybuild/easyconfigs/l/libheif/{libheif-1.12.0-GCC-11.2.0.eb => libheif-1.12.0-GCCcore-11.2.0.eb} (92%) rename easybuild/easyconfigs/l/libheif/{libheif-1.16.2-GCC-11.3.0.eb => libheif-1.16.2-GCCcore-11.3.0.eb} (93%) rename easybuild/easyconfigs/l/libheif/{libheif-1.17.6-GCC-12.3.0.eb => libheif-1.17.6-GCCcore-12.3.0.eb} (93%) diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCCcore-11.3.0.eb similarity index 91% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCCcore-11.3.0.eb index 7640cb6a545..b7fbebbccca 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.11-GCCcore-11.3.0.eb @@ -8,13 +8,14 @@ version = '1.0.11' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['2f8f12cabbdb15e53532b7c1eb964d4e15d444db1be802505e6ac97a25035bab'] builddependencies = [ + ('binutils', '2.38'), ('CMake', '3.23.1'), ] diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-12.3.0.eb similarity index 91% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-12.3.0.eb index 9d6371e84ba..7d6d8ec7ec1 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.15-GCCcore-12.3.0.eb @@ -8,13 +8,14 @@ version = '1.0.15' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['00251986c29d34d3af7117ed05874950c875dd9292d016be29d3b3762666511d'] builddependencies = [ + ('binutils', '2.40'), ('CMake', '3.26.3'), ] diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-10.3.0.eb similarity index 83% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-10.3.0.eb index 38d6c4a7d6e..3cf9fb88dc9 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-10.3.0.eb @@ -6,13 +6,16 @@ version = '1.0.8' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['24c791dd334fa521762320ff54f0febfd3c09fc978880a8c5fbc40a88f21d905'] -builddependencies = [('CMake', '3.22.1')] +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] sanity_check_paths = { 'files': ['bin/dec265', 'bin/enc265', 'lib/liblibde265.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-11.2.0.eb similarity index 83% rename from easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb rename to easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-11.2.0.eb index 647d345e73e..e2065d805b0 100644 --- a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCCcore-11.2.0.eb @@ -6,13 +6,16 @@ version = '1.0.8' homepage = 'https://github.com/strukturag/libde265' description = "libde265 is an open source implementation of the h.265 video codec" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['24c791dd334fa521762320ff54f0febfd3c09fc978880a8c5fbc40a88f21d905'] -builddependencies = [('CMake', '3.20.1')] +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] sanity_check_paths = { 'files': ['bin/dec265', 'bin/enc265', 'lib/liblibde265.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-10.3.0.eb similarity index 92% rename from easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-10.3.0.eb index 7850c1ed564..93f14603ac1 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-10.3.0.eb @@ -6,13 +6,14 @@ version = '1.12.0' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] builddependencies = [ + ('binutils', '2.36.1'), ('CMake', '3.20.1'), ('Doxygen', '1.9.1'), ] diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-11.2.0.eb similarity index 92% rename from easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-11.2.0.eb index 31a01b9b103..164821bc84e 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCCcore-11.2.0.eb @@ -6,13 +6,14 @@ version = '1.12.0' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] builddependencies = [ + ('binutils', '2.37'), ('CMake', '3.22.1'), ('Doxygen', '1.9.1'), ] diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb similarity index 93% rename from easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb index 9eb3548d709..c2051457429 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb @@ -8,13 +8,14 @@ version = '1.16.2' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['7f97e4205c0bd9f9b8560536c8bd2e841d1c9a6d610401eb3eb87ed9cdfe78ea'] builddependencies = [ + ('binutils', '2.3'), ('CMake', '3.23.1'), ('Doxygen', '1.9.4'), ] diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCCcore-12.3.0.eb similarity index 93% rename from easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb rename to easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCCcore-12.3.0.eb index 77784e13457..9ca2db177a2 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.17.6-GCCcore-12.3.0.eb @@ -8,13 +8,14 @@ version = '1.17.6' homepage = 'https://github.com/strukturag/libheif' description = "libheif is an HEIF and AVIF file format decoder and encoder" -toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['8390baf4913eda0a183e132cec62b875fb2ef507ced5ddddc98dfd2f17780aee'] builddependencies = [ + ('binutils', '2.40'), ('CMake', '3.26.3'), ('Doxygen', '1.9.7'), ] From 3a247203f82ed994ee575cbc63b146a685b3a8a9 Mon Sep 17 00:00:00 2001 From: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 18 Dec 2024 16:01:19 +0000 Subject: [PATCH 30/34] fix type --- .../easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb index c2051457429..c0a02db1292 100644 --- a/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libheif/libheif-1.16.2-GCCcore-11.3.0.eb @@ -15,7 +15,7 @@ sources = [SOURCE_TAR_GZ] checksums = ['7f97e4205c0bd9f9b8560536c8bd2e841d1c9a6d610401eb3eb87ed9cdfe78ea'] builddependencies = [ - ('binutils', '2.3'), + ('binutils', '2.38'), ('CMake', '3.23.1'), ('Doxygen', '1.9.4'), ] From 892e94bc13619683dc608b0075bbf6c205d8c8f1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 18 Dec 2024 20:00:42 +0100 Subject: [PATCH 31/34] Update easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb --- easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb index 48f991538d9..b677adb6a37 100644 --- a/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-12.0.0-GCCcore-13.2.0.eb @@ -55,7 +55,6 @@ postinstallcmds = ['rm %(installdir)s/bin/python*'] # use EB_GUROBI_LICENSE_FILE environment variable, or # uncomment and modify the following variable: # license_file = '/path/to/my-license-file' -license_file = HOME + '/licenses/%(name)s.lic' modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' From 082e64f32e91d6a4cc2c65f6eea5e52f67a6fc48 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 19 Dec 2024 13:21:44 +0000 Subject: [PATCH 32/34] Fix checksums for Safetensors-0.4.4-gfbf-2023b.eb --- .../Safetensors-0.4.4-gfbf-2023b.eb | 114 ++++++++++++++++++ 1 file changed, 114 insertions(+) diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb index 50ead1b54c1..ddaa26cbca6 100644 --- a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb @@ -139,6 +139,120 @@ crates = [ ('zerocopy-derive', '0.7.35'), ] +checksums = [ + {'aho-corasick-1.1.3.tar.gz': '8e60d3430d3a69478ad0993f19238d2df97c507009a52b3c10addcd7f6bcb916'}, + {'anes-0.1.6.tar.gz': '4b46cbb362ab8752921c97e041f5e366ee6297bd428a31275b9fcf1e380f7299'}, + {'anstyle-1.0.8.tar.gz': '1bec1de6f59aedf83baf9ff929c98f2ad654b97c9510f4e70cf6f661d49fd5b1'}, + {'autocfg-1.3.0.tar.gz': '0c4b4d0bd25bd0b74681c0ad21497610ce1b7c91b1022cd21c80c6fbdd9476b0'}, + {'bit-set-0.5.3.tar.gz': '0700ddab506f33b20a03b13996eccd309a48e5ff77d0d95926aa0210fb4e95f1'}, + {'bit-vec-0.6.3.tar.gz': '349f9b6a179ed607305526ca489b34ad0a41aed5f7980fa90eb03160b69598fb'}, + {'bitflags-2.6.0.tar.gz': 'b048fb63fd8b5923fc5aa7b340d8e156aec7ec02f0c78fa8a6ddc2613f6f71de'}, + {'bumpalo-3.16.0.tar.gz': '79296716171880943b8470b5f8d03aa55eb2e645a4874bdbb28adb49162e012c'}, + {'byteorder-1.5.0.tar.gz': '1fd0f2584146f6f2ef48085050886acf353beff7305ebd1ae69500e27c67f64b'}, + {'cast-0.3.0.tar.gz': '37b2a672a2cb129a2e41c10b1224bb368f9f37a2b16b612598138befd7b37eb5'}, + {'cfg-if-1.0.0.tar.gz': 'baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd'}, + {'ciborium-0.2.2.tar.gz': 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'1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, +] use_pip = True From 70b92492a6d186510eae785ae4e0a34d16055966 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 19 Dec 2024 14:40:25 +0000 Subject: [PATCH 33/34] add ANTLR using Java/17 and switch NCO-5.2.9-foss-2024a.eb to use it --- .../ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb | 36 +++++++++++++++++++ .../easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb | 4 +-- 2 files changed, 38 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb new file mode 100644 index 00000000000..e614536bfb5 --- /dev/null +++ b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-17.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'ANTLR' +version = '2.7.7' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.antlr2.org/' +description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) + is a language tool that provides a framework for constructing recognizers, + compilers, and translators from grammatical descriptions containing + Java, C#, C++, or Python actions.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://www.antlr2.org/download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_includes.patch'] +checksums = [ + '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz + 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch +] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Java', '17', '', SYSTEM)] + +configopts = '--disable-examples --disable-csharp --disable-python' + +sanity_check_paths = { + 'files': ['bin/antlr', 'bin/antlr-config'], + 'dirs': ['include'], +} + +sanity_check_commands = ["antlr --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb index cf83d365785..b0a8726462e 100644 --- a/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb +++ b/easybuild/easyconfigs/n/NCO/NCO-5.2.9-foss-2024a.eb @@ -4,7 +4,7 @@ name = 'NCO' version = '5.2.9' homepage = "https://github.com/nco/nco" -description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5.""" toolchain = {'name': 'foss', 'version': '2024a'} @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [ ('UDUNITS', '2.2.28'), ('expat', '2.6.2'), - ('ANTLR', '2.7.7', '-Java-21.0.2'), + ('ANTLR', '2.7.7', '-Java-17'), ('libdap', '3.21.0-131'), ('GSL', '2.8'), ('netCDF', '4.9.2'), From 57708900f71e4de2b8e997efff1abbfef4891c8f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 19 Dec 2024 14:42:26 +0000 Subject: [PATCH 34/34] remove ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb --- .../ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb diff --git a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb b/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb deleted file mode 100644 index 333a0374279..00000000000 --- a/easybuild/easyconfigs/a/ANTLR/ANTLR-2.7.7-GCCcore-13.3.0-Java-21.0.2.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'ANTLR' -version = '2.7.7' -versionsuffix = '-Java-%(javaver)s' - -homepage = 'https://www.antlr2.org/' -description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) - is a language tool that provides a framework for constructing recognizers, - compilers, and translators from grammatical descriptions containing - Java, C#, C++, or Python actions.""" - -toolchain = {'name': 'GCCcore', 'version': '13.3.0'} - -source_urls = ['https://www.antlr2.org/download/'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_includes.patch'] -checksums = [ - '853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz - 'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch -] - -builddependencies = [('binutils', '2.42')] - -dependencies = [('Java', '21.0.2', '', SYSTEM)] - -configopts = '--disable-examples --disable-csharp --disable-python' - -sanity_check_paths = { - 'files': ['bin/antlr', 'bin/antlr-config'], - 'dirs': ['include'], -} - -sanity_check_commands = ["antlr --help"] - -moduleclass = 'tools'