From 247f9dbe23f195bf0f08f9f4ee1bdc19de694d3b Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Thu, 23 Apr 2020 11:07:49 +0200 Subject: [PATCH 1/8] adding easyconfigs: artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb, rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb, gotree-0.4.0-binary.eb, goalign-0.3.2-binary.eb, IQ-TREE-1.6.12-foss-2018b.eb, Longshot-0.4.1-foss-2018b.eb, MAFFT-7.427-foss-2018b-with-extensions.eb, MUSCLE-3.8.1551-foss-2018b.eb, nodejs-12.16.1-GCCcore-7.3.0.eb, Rust-1.42.0-GCCcore-7.3.0.eb --- ...20.04.13-foss-2018b-Python-3.6.6-medaka.eb | 133 ++++++++++++++++++ .../g/goalign/goalign-0.3.2-binary.eb | 28 ++++ .../g/gotree/gotree-0.4.0-binary.eb | 28 ++++ .../i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb | 34 +++++ .../l/Longshot/Longshot-0.4.1-foss-2018b.eb | 40 ++++++ .../MAFFT-7.427-foss-2018b-with-extensions.eb | 38 +++++ .../m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb | 30 ++++ .../n/nodejs/nodejs-12.16.1-GCCcore-7.3.0.eb | 44 ++++++ .../r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb | 28 ++++ ...ampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb | 68 +++++++++ 10 files changed, 471 insertions(+) create mode 100644 easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb create mode 100644 easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb create mode 100644 easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb create mode 100644 easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb create mode 100644 easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-foss-2018b-with-extensions.eb create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-12.16.1-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb create mode 100644 easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb new file mode 100644 index 00000000000..ccea25cd45c --- /dev/null +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb @@ -0,0 +1,133 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'artic-ncov2019' +# commit 4a7461c3cc9865860d69223ba8360df13a248f13 +version = '2020.04.13' + +local_python_versionsuffix = '-Python-%(pyver)s' +versionsuffix = local_python_versionsuffix + '-medaka' + +homepage = "https://github.com/artic-network/artic-ncov2019" +description = """Initial implementation of an ARTIC bioinformatics platform +for nanopore sequencing of nCoV2019 novel coronavirus.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('Python', '3.6.6'), # pandas, + ('Biopython', '1.72', local_python_versionsuffix), + ('Pysam', '0.15.1', local_python_versionsuffix), + ('BWA', '0.7.17'), + ('Eigen', '3.3.7', '', True), + ('minimap2', '2.13'), + ('SAMtools', '1.9'), + ('MUSCLE', '3.8.1551'), + ('ETE', '3.1.1', local_python_versionsuffix), + ('MAFFT', '7.427', '-with-extensions'), + ('IQ-TREE', '1.6.12'), + ('snakemake', '5.2.4', local_python_versionsuffix), + ('Longshot', '0.4.1'), + ('medaka', '0.11.4', local_python_versionsuffix), + ('python-parasail', '1.1.16', local_python_versionsuffix), + ('PhyML', '3.3.20190321'), + ('nodejs', '12.16.1'), + ('goalign', '0.3.2', '-binary', True), + ('gotree', '0.4.0', '-binary', True), + ('rampart', '1.2.0rc3', local_python_versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('zipp', '1.0.0', { + 'checksums': ['d38fbe01bbf7a3593a32bc35a9c4453c32bc42b98c377f9bff7e9f8da157786c'], + }), + ('pluggy', '0.13.1', { + 'checksums': ['15b2acde666561e1298d71b523007ed7364de07029219b604cf808bfa1c765b0'], + }), + ('py', '1.8.1', { + 'checksums': ['5e27081401262157467ad6e7f851b7aa402c5852dbcb3dae06768434de5752aa'], + }), + ('wcwidth', '0.1.9', { + 'checksums': ['ee73862862a156bf77ff92b09034fc4825dd3af9cf81bc5b360668d425f3c5f1'], + }), + ('attrs', '19.3.0', { + 'modulename': 'attr', + 'checksums': ['f7b7ce16570fe9965acd6d30101a28f62fb4a7f9e926b3bbc9b61f8b04247e72'], + }), + ('importlib-metadata', '1.6.0', { + 'modulename': 'importlib_metadata', + 'source_tmpl': 'importlib_metadata-%(version)s.tar.gz', + 'checksums': ['34513a8a0c4962bc66d35b359558fd8a5e10cd472d37aec5f66858addef32c1e'], + }), + ('more-itertools', '8.2.0', { + 'modulename': 'more_itertools', + 'checksums': ['b1ddb932186d8a6ac451e1d95844b382f55e12686d51ca0c68b6f61f2ab7a507'], + }), + ('packaging', '14.5', { + 'checksums': ['363f9193daa14085b8dfeeb2bf64227bcf1dc85c02ae2a5c6018b01f77e46491'], + }), + ('args', '0.1.0', { + 'checksums': ['a785b8d837625e9b61c39108532d95b85274acd679693b71ebb5156848fcf814'], + }), + ('pytest', '5.4.1', { + 'checksums': ['84dde37075b8805f3d1f392cc47e38a0e59518fb46a431cfdaf7cf1ce805f970'], + }), + ('tqdm', '4.45.0', { + 'checksums': ['00339634a22c10a7a22476ee946bbde2dbe48d042ded784e4d88e0236eca5d81'], + }), + ('fieldbioinformatics', '1.1.0-rc2', { + 'modulename': False, + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], + 'checksums': ['7083f67b1188e8f9b55f8bd4f7a46853e9c74ae7dde324b1fc8e792a85e58073'], + }), + ('Porechop', '0.3.2pre', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/Porechop/archive'], + 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], + }), + ('binlorry', '1.3.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['0aabdc2546a0dc7f298cc5c8b8c27e648a92c93f03d21ac424a7a845fc13ef5c'], + }), + ('clint', '0.5.1', { + 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], + }), + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('PyVCF', '0.6.8', { + 'modulename': 'vcf', + 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], + }), +] + +components = [ + (name, version, { + 'easyblock': 'Tarball', + 'source_urls': ['https://github.com/artic-network/artic-ncov2019/archive/'], + 'sources': [{ + 'download_filename': '4a7461c3cc9865860d69223ba8360df13a248f13.tar.gz', + 'filename': SOURCE_TAR_GZ, + }], + 'checksums': ['26bc96742e291795d4a7c1154336715d98168d8ce3524ad7adfea0b5562eb34d'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'artic -v', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb b/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb new file mode 100644 index 00000000000..dacfab7ed17 --- /dev/null +++ b/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb @@ -0,0 +1,28 @@ +easyblock = 'Binary' + +name = 'goalign' +version = '0.3.2' +versionsuffix = "-binary" + +homepage = 'https://github.com/evolbioinfo/goalign/' +description = "Goalign is a set of command line tools to manipulate multiple alignments." + +toolchain = SYSTEM + +source_urls = ['https://github.com/evolbioinfo/goalign/releases/download/v%(version)s'] +sources = ['goalign_amd64_linux'] +checksums = ['a0453c63b9c299e9d775ec9b3afe9bac33984bf14a8bcfcdbfa784e4879601d0'] + +postinstallcmds = [ + "ln -s %(installdir)s/%(name)s_amd64_linux %(installdir)s/%(name)s", +] +sanity_check_paths = { + 'files': ['%(name)s_amd64_linux'], + 'dirs': [], +} + +sanity_check_commands = [ + 'goalign --help' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb b/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb new file mode 100644 index 00000000000..d8db557db07 --- /dev/null +++ b/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb @@ -0,0 +1,28 @@ +easyblock = 'Binary' + +name = 'gotree' +version = '0.4.0' +versionsuffix = "-binary" + +homepage = 'https://github.com/evolbioinfo/gotree/' +description = "GoTree is a set of command line tools to manipulate phylogenetic trees." + +toolchain = SYSTEM + +source_urls = ['https://github.com/evolbioinfo/gotree/releases/download/v%(version)s'] +sources = ['gotree_amd64_linux'] +checksums = ['8527cc7082dfc46f03a1a49e02cd07da7cef94112f0b85c43de3416d53dcb188'] + +postinstallcmds = [ + "ln -s %(installdir)s/%(name)s_amd64_linux %(installdir)s/%(name)s", +] +sanity_check_paths = { + 'files': ['%(name)s_amd64_linux'], + 'dirs': [], +} + +sanity_check_commands = [ + 'gotree --help' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb new file mode 100644 index 00000000000..7a41be58181 --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '1.6.12' + +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'foss', 'version': '2018b'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary +# toolchainopts = {'usempi': True} + +github_account = 'Cibiv' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['9614092de7a157de82c9cc402b19cc8bfa0cb0ffc93b91817875c2b4bb46a284'] + +builddependencies = [ + ('CMake', '3.12.1'), + ('Eigen', '3.3.7', '', True), +] +dependencies = [('zlib', '1.2.11')] + +configopts = [ + '-DIQTREE_FLAGS=omp', + '-DIQTREE_FLAGS=mpi', +] + +sanity_check_paths = { + 'files': ['bin/iqtree', 'bin/iqtree-mpi'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb new file mode 100644 index 00000000000..f44bdff2d02 --- /dev/null +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb @@ -0,0 +1,40 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +easyblock = 'Binary' + +name = 'Longshot' +version = '0.4.1' + +homepage = 'https://github.com/pjedge/longshot' +description = """Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific + Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs + a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can + be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://github.com/pjedge/longshot/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['062529eb47fafc2ef4a1a12ea30a565a0df922b310b6fc5705a1605ce4f495f3'] + +builddependencies = [ + ('binutils', '2.30'), + ('Rust', '1.42.0'), + ('Clang', '7.0.1'), + ('zlib', '1.2.11'), + ('XZ', '5.2.4'), +] + +extract_sources = True + +# https://github.com/rust-bio/rust-htslib/issues/112 +install_cmd = "export LIBCLANG_PATH=${EBROOTCLANG}/lib && " +install_cmd += "cargo install --root %(installdir)s --path ." + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-foss-2018b-with-extensions.eb b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-foss-2018b-with-extensions.eb new file mode 100644 index 00000000000..4c69ab01998 --- /dev/null +++ b/easybuild/easyconfigs/m/MAFFT/MAFFT-7.427-foss-2018b-with-extensions.eb @@ -0,0 +1,38 @@ +# 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 +# 7.305 modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'MAFFT' +version = '7.427' +versionsuffix = '-with-extensions' + +homepage = 'https://mafft.cbrc.jp/alignment/software/source.html' +description = """MAFFT is a multiple sequence alignment program + for unix-like operating systems. It offers a range of multiple + alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), + FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://mafft.cbrc.jp/alignment/software/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s-src.tgz'] +checksums = ['068abcbc20965cbfa4e14c138cbfbcd0d311874ac2fdde384a580ac774f40e26'] + +skipsteps = ['configure'] +start_dir = 'core' +installopts = 'PREFIX=%(installdir)s' + +modextrapaths = {'MAFFT_BINARIES': 'libexec/mafft'} + +sanity_check_paths = { + 'files': ['bin/mafft'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb new file mode 100644 index 00000000000..fdb6af2845b --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = "3.8.1551" + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = ['https://www.drive5.com/muscle/'] +sources = ['%(namelower)s_src_%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-mk-hardcoding.patch'] +checksums = [ + 'c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e', # muscle_src_3.8.1551.tar.gz + '5c38f93dcb03f769ecea7e21c83671920d0f3a88102ac6e0a51df23c33414766', # MUSCLE-3.8.1551_fix-mk-hardcoding.patch +] + +files_to_copy = [(["muscle"], 'bin')] + +sanity_check_paths = { + 'files': ["bin/%(namelower)s"], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-12.16.1-GCCcore-7.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-12.16.1-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..a68fc577392 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-12.16.1-GCCcore-7.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '12.16.1' # 12.16.1 was LTS on 2020-05-22 +local_libversion = '72' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['http://%(name)s.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['4fe8c3454f9bee5bbe72d44aa25cd931859b3037b7a9473081b3b2bd1b465b95'] + +builddependencies = [ + ('binutils', '2.30'), + ('Python', '2.7.15', '-bare'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'dirs': ['lib/node_modules', 'include/node'] +} + +modextrapaths = {'CPATH': 'include/node'} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..6f7bdda2b6b --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.42.0-GCCcore-7.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.42.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +checksums = ['d2e8f931d16a0539faaaacd801e0d92c58df190269014b2360c6ab2a90ee3475'] + +builddependencies = [ + ('binutils', '2.30'), + ('CMake', '3.12.1'), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc" + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..3f51c302b5d --- /dev/null +++ b/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,68 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'rampart' +version = '1.2.0rc3' + +versionsuffix = '-Python-%(pyver)s' + +homepage = "https://github.com/artic-network/rampart/" +description = "Read Assignment, Mapping, and Phylogenetic Analysis in Real Time." +toolchain = {'name': 'foss', 'version': '2018b'} + +dependencies = [ + ('nodejs', '12.16.1'), + ('Python', '3.6.6'), # pandas, + ('Biopython', '1.72', versionsuffix), + ('snakemake', '5.2.4', versionsuffix), + ('minimap2', '2.13'), +] + +use_pip = True +sanity_pip_check = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('Porechop', '0.3.2pre', { + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/artic-network/Porechop/archive'], + 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], + }), + ('binlorry', '1.3.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'unpack_sources': False, + 'checksums': ['0aabdc2546a0dc7f298cc5c8b8c27e648a92c93f03d21ac424a7a845fc13ef5c'], + }), +] + +# Don't ever try to install unpacked source of nodejs globally! +# Always use 'npm install -g downloaded_file.tar.gz` or you will end up having broken links and installation will fail. +# -d (debug) and --timing can show errors while downloading dependencies +local_install_cmd = "npm install -d --timing --prefix %(installdir)s -g v%(version)s.tar.gz" + +components = [ + (name, version, { + 'easyblock': 'Binary', + 'source_urls': ['https://github.com/artic-network/rampart/archive/'], + 'sources': [{ + 'filename': 'v%(version)s.tar.gz', + # Don't extract downloaded .tar.gz, just copy that to builddir + 'extract_cmd': "cp %s .", + }], + 'checksums': ['c7696257af96618d05607bd015b5393b8c0827cfee10f4562e4adad5a1bd74f4'], + 'install_cmd': local_install_cmd, + }), +] + +sanity_check_paths = { + 'files': ['bin/binlorry', 'bin/porechop'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [ + 'rampart --help' +] + +moduleclass = 'bio' From dc2295443073e5a8e6ae9083828ac206aa9f7a06 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Fri, 24 Apr 2020 14:01:40 +0200 Subject: [PATCH 2/8] reworked, fixed remarks --- ...019-2020.04.13-foss-2018b-Python-3.6.6.eb} | 42 +++++++++------ .../g/goalign/goalign-0.3.2-binary.eb | 28 ---------- .../g/gotree/gotree-0.4.0-binary.eb | 28 ---------- .../i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb | 2 +- ...8b.eb => Longshot-0.4.1-GCC-7.3.0-2.30.eb} | 2 +- .../libdeflate-1.5-GCCcore-7.3.0.eb | 43 +++++++++++++++ ...b.eb => MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb} | 2 +- ...nopolish-0.13.1-foss-2018b-Python-3.6.6.eb | 53 +++++++++++++++++++ ...ampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb | 9 ++-- 9 files changed, 130 insertions(+), 79 deletions(-) rename easybuild/easyconfigs/a/artic-ncov2019/{artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb => artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb} (77%) delete mode 100644 easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb delete mode 100644 easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb rename easybuild/easyconfigs/l/Longshot/{Longshot-0.4.1-foss-2018b.eb => Longshot-0.4.1-GCC-7.3.0-2.30.eb} (96%) create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb rename easybuild/easyconfigs/m/MUSCLE/{MUSCLE-3.8.1551-foss-2018b.eb => MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb} (95%) create mode 100644 easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb similarity index 77% rename from easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb rename to easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb index ccea25cd45c..cfd5da43056 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6-medaka.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb @@ -7,8 +7,7 @@ name = 'artic-ncov2019' # commit 4a7461c3cc9865860d69223ba8360df13a248f13 version = '2020.04.13' -local_python_versionsuffix = '-Python-%(pyver)s' -versionsuffix = local_python_versionsuffix + '-medaka' +versionsuffix = '-Python-%(pyver)s' homepage = "https://github.com/artic-network/artic-ncov2019" description = """Initial implementation of an ARTIC bioinformatics platform @@ -18,25 +17,29 @@ toolchain = {'name': 'foss', 'version': '2018b'} dependencies = [ ('Python', '3.6.6'), # pandas, - ('Biopython', '1.72', local_python_versionsuffix), - ('Pysam', '0.15.1', local_python_versionsuffix), + ('Biopython', '1.72', versionsuffix), + ('Pysam', '0.15.1', versionsuffix), ('BWA', '0.7.17'), ('Eigen', '3.3.7', '', True), ('minimap2', '2.13'), ('SAMtools', '1.9'), ('MUSCLE', '3.8.1551'), - ('ETE', '3.1.1', local_python_versionsuffix), + ('ETE', '3.1.1', versionsuffix), ('MAFFT', '7.427', '-with-extensions'), ('IQ-TREE', '1.6.12'), - ('snakemake', '5.2.4', local_python_versionsuffix), + ('snakemake', '5.2.4', versionsuffix), ('Longshot', '0.4.1'), - ('medaka', '0.11.4', local_python_versionsuffix), - ('python-parasail', '1.1.16', local_python_versionsuffix), + ('medaka', '0.11.4', versionsuffix), + ('python-parasail', '1.1.16', versionsuffix), ('PhyML', '3.3.20190321'), ('nodejs', '12.16.1'), - ('goalign', '0.3.2', '-binary', True), - ('gotree', '0.4.0', '-binary', True), - ('rampart', '1.2.0rc3', local_python_versionsuffix), + ('goalign', '0.3.2', '', True), + ('gotree', '0.4.0', '', True), + ('rampart', '1.2.0rc3', versionsuffix), + ('libdeflate', '1.5'), + ('nanopolish', '0.13.1', versionsuffix), + ('seqtk', '1.3'), + ('BCFtools', '1.9'), ] use_pip = True @@ -88,15 +91,16 @@ exts_list = [ 'source_urls': ['https://github.com/artic-network/fieldbioinformatics/archive'], 'checksums': ['7083f67b1188e8f9b55f8bd4f7a46853e9c74ae7dde324b1fc8e792a85e58073'], }), + # This is not upstream version, but artic tweaked one, which is exactly required. ('Porechop', '0.3.2pre', { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/artic-network/Porechop/archive'], 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], }), ('binlorry', '1.3.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['0aabdc2546a0dc7f298cc5c8b8c27e648a92c93f03d21ac424a7a845fc13ef5c'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/rambaut/binlorry/archive'], + 'checksums': ['001b74cad497b7253b821ceaac8c0b829b2787396a896fc2d3940a704a149b48'], }), ('clint', '0.5.1', { 'checksums': ['05224c32b1075563d0b16d0015faaf9da43aa214e4a2140e51f08789e7a4c5aa'], @@ -108,6 +112,10 @@ exts_list = [ 'modulename': 'vcf', 'checksums': ['e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9'], }), + ('ont-fast5-api', '3.1.1', { + 'modulename': 'ont_fast5_api', + 'checksums': ['ce5a955c5e90a393f040fb36fc461382339fc0b9cd63e3969b9763127dc2b0d3'], + }), ] components = [ @@ -121,9 +129,11 @@ components = [ 'checksums': ['26bc96742e291795d4a7c1154336715d98168d8ce3524ad7adfea0b5562eb34d'], }), ] - +local_artic_bins = [ + 'artic', 'artic_fasta_header', 'artic_make_depth_mask', 'artic_mask', 'artic_vcf_filter', 'artic_vcf_merge' +] sanity_check_paths = { - 'files': [], + 'files': ['bin/%s' % f for f in local_artic_bins], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ diff --git a/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb b/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb deleted file mode 100644 index dacfab7ed17..00000000000 --- a/easybuild/easyconfigs/g/goalign/goalign-0.3.2-binary.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'Binary' - -name = 'goalign' -version = '0.3.2' -versionsuffix = "-binary" - -homepage = 'https://github.com/evolbioinfo/goalign/' -description = "Goalign is a set of command line tools to manipulate multiple alignments." - -toolchain = SYSTEM - -source_urls = ['https://github.com/evolbioinfo/goalign/releases/download/v%(version)s'] -sources = ['goalign_amd64_linux'] -checksums = ['a0453c63b9c299e9d775ec9b3afe9bac33984bf14a8bcfcdbfa784e4879601d0'] - -postinstallcmds = [ - "ln -s %(installdir)s/%(name)s_amd64_linux %(installdir)s/%(name)s", -] -sanity_check_paths = { - 'files': ['%(name)s_amd64_linux'], - 'dirs': [], -} - -sanity_check_commands = [ - 'goalign --help' -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb b/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb deleted file mode 100644 index d8db557db07..00000000000 --- a/easybuild/easyconfigs/g/gotree/gotree-0.4.0-binary.eb +++ /dev/null @@ -1,28 +0,0 @@ -easyblock = 'Binary' - -name = 'gotree' -version = '0.4.0' -versionsuffix = "-binary" - -homepage = 'https://github.com/evolbioinfo/gotree/' -description = "GoTree is a set of command line tools to manipulate phylogenetic trees." - -toolchain = SYSTEM - -source_urls = ['https://github.com/evolbioinfo/gotree/releases/download/v%(version)s'] -sources = ['gotree_amd64_linux'] -checksums = ['8527cc7082dfc46f03a1a49e02cd07da7cef94112f0b85c43de3416d53dcb188'] - -postinstallcmds = [ - "ln -s %(installdir)s/%(name)s_amd64_linux %(installdir)s/%(name)s", -] -sanity_check_paths = { - 'files': ['%(name)s_amd64_linux'], - 'dirs': [], -} - -sanity_check_commands = [ - 'gotree --help' -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb index 7a41be58181..aec8a7ac610 100644 --- a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-1.6.12-foss-2018b.eb @@ -3,12 +3,12 @@ easyblock = 'CMakeMake' name = 'IQ-TREE' version = '1.6.12' +# HTTPS is not working homepage = 'http://www.iqtree.org/' description = """Efficient phylogenomic software by maximum likelihood""" toolchain = {'name': 'foss', 'version': '2018b'} # Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary -# toolchainopts = {'usempi': True} github_account = 'Cibiv' source_urls = [GITHUB_SOURCE] diff --git a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb similarity index 96% rename from easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb rename to easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb index f44bdff2d02..48e2eb9f6a2 100644 --- a/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-foss-2018b.eb +++ b/easybuild/easyconfigs/l/Longshot/Longshot-0.4.1-GCC-7.3.0-2.30.eb @@ -10,7 +10,7 @@ description = """Longshot is a variant calling tool for diploid genomes using lo a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['https://github.com/pjedge/longshot/archive'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb new file mode 100644 index 00000000000..4622b6cfa9d --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.5' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '7.3.0'} + +# https://github.com/ebiggers/libdeflate +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['45b1b2332f443b705c59d06a49be009827291d2c487b076dc8ec2791eff4c711'] + +builddependencies = [ + ('binutils', '2.30'), + # ('Autotools', '20180311'), + # ('xorg-macros', '1.19.2'), +] + +skipsteps = ['configure'] +buildopts = 'PREFIX="%(installdir)s" CFLAGS="$CFLAGS" CPPFLAGS="$CPPFLAGS" LDFLAGS="$LDFLAGS"' +installopts = 'PREFIX="%(installdir)s" CFLAGS="$CFLAGS" CPPFLAGS="$CPPFLAGS" LDFLAGS="$LDFLAGS"' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb similarity index 95% rename from easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb rename to easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb index fdb6af2845b..6aff9d1e1c9 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-foss-2018b.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb @@ -10,7 +10,7 @@ description = """MUSCLE is one of the best-performing multiple alignment program learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks.""" -toolchain = {'name': 'foss', 'version': '2018b'} +toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} source_urls = ['https://www.drive5.com/muscle/'] sources = ['%(namelower)s_src_%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb new file mode 100644 index 00000000000..8bfbce42b87 --- /dev/null +++ b/easybuild/easyconfigs/n/nanopolish/nanopolish-0.13.1-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,53 @@ +easyblock = 'MakeCp' + +name = 'nanopolish' +version = '0.13.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/jts/nanopolish' +description = "Software package for signal-level analysis of Oxford Nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [ + 'https://github.com/jts/nanopolish/archive/', + 'https://github.com/mateidavid/fast5/archive/', +] +sources = [ + {'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}, + {'download_filename': 'v0.6.5.tar.gz', 'filename': 'fast5-v0.6.5.tar.gz'}, +] +checksums = [ + '0cf0a6aea3d3b0dd81fa8877618b12bb45e2a39b2ec2fbfc6bc0df77084a7fac', # nanopolish-0.13.1.tar.gz + 'f8b1ce2c07adb56b4f13337ef008e124255f86cdb7e74e4233afa8dca878ee1a', # fast5-v0.6.5.tar.gz +] + +builddependencies = [('Eigen', '3.3.7', '', True)] + +dependencies = [ + ('zlib', '1.2.11'), + ('HDF5', '1.10.2'), + ('HTSlib', '1.9'), + ('Python', '3.6.6'), + ('Biopython', '1.72', versionsuffix), + ('Pysam', '0.15.1', versionsuffix), + ('minimap2', '2.13'), +] + +prebuildopts = "rmdir fast5 && ln -s %(builddir)s/fast5-*/ fast5 && " +buildopts = "HDF5=noinstall EIGEN=noinstall HTS=noinstall MINIMAP2=noinstall" + +runtest = 'test ' + buildopts + +files_to_copy = [(['nanopolish'], 'bin'), 'scripts'] + +postinstallcmds = ["chmod a+rx %(installdir)s/scripts/*"] + +sanity_check_paths = { + 'files': ['bin/nanopolish'], + 'dirs': ['scripts'], +} + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb index 3f51c302b5d..112305de8b9 100644 --- a/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/r/rampart/rampart-1.2.0rc3-foss-2018b-Python-3.6.6.eb @@ -26,15 +26,16 @@ sanity_pip_check = True exts_default_options = {'source_urls': [PYPI_SOURCE]} exts_list = [ + # This is not upstream version, but artic tweaked one, which is exactly required. ('Porechop', '0.3.2pre', { 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/artic-network/Porechop/archive'], 'checksums': ['85980d6f37d38a44c66182e7b39bad487211ccfd8cb820c866ceed7ef7a15523'], }), ('binlorry', '1.3.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'unpack_sources': False, - 'checksums': ['0aabdc2546a0dc7f298cc5c8b8c27e648a92c93f03d21ac424a7a845fc13ef5c'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/rambaut/binlorry/archive'], + 'checksums': ['001b74cad497b7253b821ceaac8c0b829b2787396a896fc2d3940a704a149b48'], }), ] @@ -58,7 +59,7 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/binlorry', 'bin/porechop'], + 'files': ['bin/binlorry', 'bin/porechop', 'bin/rampart'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ From 4facf9f9007b25b8981b8f8d680cb6abef889c84 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Wed, 29 Apr 2020 09:28:46 +0200 Subject: [PATCH 3/8] changed deps version to match toolchain --- .../artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb index cfd5da43056..c010e850d20 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb @@ -20,10 +20,10 @@ dependencies = [ ('Biopython', '1.72', versionsuffix), ('Pysam', '0.15.1', versionsuffix), ('BWA', '0.7.17'), - ('Eigen', '3.3.7', '', True), + ('Eigen', '3.3.4', '', True), ('minimap2', '2.13'), ('SAMtools', '1.9'), - ('MUSCLE', '3.8.1551'), + ('MUSCLE', '3.8.31'), ('ETE', '3.1.1', versionsuffix), ('MAFFT', '7.427', '-with-extensions'), ('IQ-TREE', '1.6.12'), From d6d0ae163d891e8ab44a93549b178af128191409 Mon Sep 17 00:00:00 2001 From: darkless Date: Wed, 29 Apr 2020 09:30:03 +0200 Subject: [PATCH 4/8] added rampart/artic-ncov2019 exceptions --- test/easyconfigs/easyconfigs.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index baa53f7d8c0..9a379523bc9 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -257,8 +257,10 @@ def check_dep_vars(self, dep, dep_vars): # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) # both scVelo and Python-Geometric depend on numba 'LLVM': (r'8\.', [r'numba-0\.47\.0-', r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[34]\.2']), - # medaka 0.11.4/0.12.0requires recent TensorFlow <= 1.14 (and Python 3.6) - 'TensorFlow': ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-']), + # medaka 0.11.4/0.12.0requires recent TensorFlow <= 1.14 (and Python 3.6), artic-ncov2019 requires medaka + 'TensorFlow': ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), + # rampart requires nodejs > 10, artic-ncov2019 requires rampart + 'nodejs': ('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13']), } if dep in old_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): From c7a1a9852fe92a1eac026e4e0da216ca3c67c348 Mon Sep 17 00:00:00 2001 From: Pavel Grochal Date: Wed, 29 Apr 2020 09:59:25 +0200 Subject: [PATCH 5/8] changed MUSCLE easyconfig --- ...C-7.3.0-2.30.eb => MUSCLE-3.8.31-GCC-7.3.0-2.30.eb} | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/MUSCLE/{MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb => MUSCLE-3.8.31-GCC-7.3.0-2.30.eb} (68%) diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCC-7.3.0-2.30.eb similarity index 68% rename from easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb rename to easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCC-7.3.0-2.30.eb index 6aff9d1e1c9..25e5e69d78a 100644 --- a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.1551-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-3.8.31-GCC-7.3.0-2.30.eb @@ -1,7 +1,7 @@ easyblock = 'MakeCp' name = 'MUSCLE' -version = "3.8.1551" +version = "3.8.31" homepage = 'https://drive5.com/muscle/' description = """MUSCLE is one of the best-performing multiple alignment programs @@ -12,12 +12,12 @@ description = """MUSCLE is one of the best-performing multiple alignment program toolchain = {'name': 'GCC', 'version': '7.3.0-2.30'} -source_urls = ['https://www.drive5.com/muscle/'] -sources = ['%(namelower)s_src_%(version)s.tar.gz'] +source_urls = ['http://www.drive5.com/muscle/downloads%(version)s/'] +sources = ['%(namelower)s%(version)s_src.tar.gz'] patches = ['%(name)s-%(version)s_fix-mk-hardcoding.patch'] checksums = [ - 'c70c552231cd3289f1bad51c9bd174804c18bb3adcf47f501afec7a68f9c482e', # muscle_src_3.8.1551.tar.gz - '5c38f93dcb03f769ecea7e21c83671920d0f3a88102ac6e0a51df23c33414766', # MUSCLE-3.8.1551_fix-mk-hardcoding.patch + '43c5966a82133bd7da5921e8142f2f592c2b5f53d802f0527a2801783af809ad', # muscle3.8.31_src.tar.gz + 'e108d1cc2d394236f839facc1304ff96c0e11f7fdd6d2444761808ec860cd58a', # MUSCLE-3.8.31_fix-mk-hardcoding.patch ] files_to_copy = [(["muscle"], 'bin')] From 9d630f601d97a21625466ab9b46b64c2b79e7779 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 10:50:33 +0200 Subject: [PATCH 6/8] add variable for commit used in artic-ncov2019 easyconfig --- .../artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb index c010e850d20..de8a9ab2b28 100644 --- a/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/a/artic-ncov2019/artic-ncov2019-2020.04.13-foss-2018b-Python-3.6.6.eb @@ -4,7 +4,7 @@ easyblock = 'PythonBundle' name = 'artic-ncov2019' -# commit 4a7461c3cc9865860d69223ba8360df13a248f13 +local_commit = '4a7461c3cc9865860d69223ba8360df13a248f13' version = '2020.04.13' versionsuffix = '-Python-%(pyver)s' @@ -123,7 +123,7 @@ components = [ 'easyblock': 'Tarball', 'source_urls': ['https://github.com/artic-network/artic-ncov2019/archive/'], 'sources': [{ - 'download_filename': '4a7461c3cc9865860d69223ba8360df13a248f13.tar.gz', + 'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ, }], 'checksums': ['26bc96742e291795d4a7c1154336715d98168d8ce3524ad7adfea0b5562eb34d'], From dff098c82fee69854270eb0cd6acd46047cb2ba7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 10:50:56 +0200 Subject: [PATCH 7/8] clean up commented out build dependencies in libdeflate easyconfig --- .../l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb index 4622b6cfa9d..4e7cad2274f 100644 --- a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.5-GCCcore-7.3.0.eb @@ -17,11 +17,7 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['45b1b2332f443b705c59d06a49be009827291d2c487b076dc8ec2791eff4c711'] -builddependencies = [ - ('binutils', '2.30'), - # ('Autotools', '20180311'), - # ('xorg-macros', '1.19.2'), -] +builddependencies = [('binutils', '2.30')] skipsteps = ['configure'] buildopts = 'PREFIX="%(installdir)s" CFLAGS="$CFLAGS" CPPFLAGS="$CPPFLAGS" LDFLAGS="$LDFLAGS"' From e62ddf85f0fcb131ad468f821bccd69762016bf1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 29 Apr 2020 10:52:16 +0200 Subject: [PATCH 8/8] add missing space in comment --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9a379523bc9..5efed20d6a8 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -257,7 +257,7 @@ def check_dep_vars(self, dep, dep_vars): # numba 0.47.x requires LLVM 7.x or 8.x (see https://github.com/numba/llvmlite#compatibility) # both scVelo and Python-Geometric depend on numba 'LLVM': (r'8\.', [r'numba-0\.47\.0-', r'scVelo-0\.1\.24-', r'PyTorch-Geometric-1\.[34]\.2']), - # medaka 0.11.4/0.12.0requires recent TensorFlow <= 1.14 (and Python 3.6), artic-ncov2019 requires medaka + # medaka 0.11.4/0.12.0 requires recent TensorFlow <= 1.14 (and Python 3.6), artic-ncov2019 requires medaka 'TensorFlow': ('1.13.1;', ['medaka-0.11.4-', 'medaka-0.12.0-', 'artic-ncov2019-2020.04.13']), # rampart requires nodejs > 10, artic-ncov2019 requires rampart 'nodejs': ('12.16.1', ['rampart-1.2.0rc3-', 'artic-ncov2019-2020.04.13']),