diff --git a/280_anvio/ETE-3.1.3-foss-2023a.eb b/280_anvio/ETE-3.1.3-foss-2023a.eb new file mode 100644 index 00000000..be10b633 --- /dev/null +++ b/280_anvio/ETE-3.1.3-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.3' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +patches = ['ETE-3.1.2-foss-2021b_fix_binpath.patch'] +checksums = [ + {'ete3-3.1.3.tar.gz': '06a3b7fa8ed90187b076a8dbbe5b1b62acee94201d3c6e822f55f449601ef6f2'}, + {'ETE-3.1.2-foss-2021b_fix_binpath.patch': 'f71d1135e87e1035736f67b92ebcfebd2ae4d57e48f45e25c1a6144c60f11fbd'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('lxml', '4.9.2'), + ('PyQt5', '5.15.10'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/280_anvio/Pysam-0.22.0-GCC-12.3.0.eb b/280_anvio/Pysam-0.22.0-GCC-12.3.0.eb new file mode 100755 index 00000000..684f6806 --- /dev/null +++ b/280_anvio/Pysam-0.22.0-GCC-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.22.0' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f'] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('ncurses', '6.4'), + ('cURL', '8.0.1'), + ('XZ', '5.4.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/280_anvio/anvio.eb b/280_anvio/anvio.eb new file mode 100644 index 00000000..b7196317 --- /dev/null +++ b/280_anvio/anvio.eb @@ -0,0 +1,95 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'anvio' +version = '8' + +homepage = 'https://merenlab.org/software/anvio/' +description = """An analysis and visualization platform for 'omics data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'merenlab' + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pysam', '0.22.0'), + ('scikit-learn', '1.3.1'), + ('matplotlib', '3.7.2'), + ('prodigal', '2.6.3-20230127'), + ('Biopython', '1.83'), + ('h5py', '3.9.0'), + ('HMMER', '3.4'), + ('networkx', '3.1'), + ('numba', '0.58.1'), + ('statsmodels', '0.14.1'), + ('snakemake', '8.4.2'), + ('ETE', '3.1.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bottle', '0.12.25', { + 'checksums': ['e1a9c94970ae6d710b3fb4526294dfeb86f2cb4a81eff3a4b98dc40fb0e5e021'], + }), + ('colored', '2.2.4', { + 'checksums': ['595e1dd7f3b472ea5f12af21d2fec8a2ea2cf8f9d93e67180197330b26df9b61'], + }), + ('Django', '5.0.1', { + 'checksums': ['8c8659665bc6e3a44fefe1ab0a291e5a3fb3979f9a8230be29de975e57e8f854'], + }), + ('illumina-utils', '2.13', { + 'checksums': ['e688ca221ea6178614073b72205fce7b4a54695237c7aa96713492ecd99bd56e'], + }), + ('mistune', '3.0.2', { + 'checksums': ['fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8'], + }), + ('multiprocess', '0.70.16', { + 'checksums': ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'], + }), + ('Paste', '3.7.1', { + 'checksums': ['6d07a8e1c7fa72b8cf403762a002f80d12c0384056956dd0a87cb9a3be64749a'], + }), + ('plotext', '5.2.8', { + 'checksums': ['319a287baabeb8576a711995f973a2eba631c887aa6b0f33ab016f12c50ffebe'], + }), + ('pyani', '0.2.12', { + 'checksums': ['4f56b217656f53416b333b69495a4ba8cde782e64e475e1481cb2213ce6b9388'], + }), + ('rich_argparse', '1.4.0', { + 'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'], + }), + (name, version, { + # remove too strict requirements for Python packages anvio depends on + 'preinstallopts': "sed -i -e 's/==/>=/g' -e 's/<=.*//g' requirements.txt && ", + 'source_urls': ['https://github.com/merenlab/anvio/releases/download/v%(version)s/'], + 'checksums': ['13da84d48d7266a8986815efb024772fa26ad1c8a951d42897c3a51e3d924feb'], + }), +] + +local_binaries_list = [ + 'anvi-pan-genome', + 'anvi-script-reformat-fasta', + 'anvi-profile', + 'anvi-help', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries_list], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'anvi-self-test --suite mini', + 'anvi-pan-genome --help', + 'anvi-script-reformat-fasta --help', + 'anvi-profile --version', + 'anvi-help --help', +] + +moduleclass = 'bio' diff --git a/280_anvio/prodigal-2.6.3-20230127-GCCcore-12.3.0.eb b/280_anvio/prodigal-2.6.3-20230127-GCCcore-12.3.0.eb new file mode 100644 index 00000000..9484ddf4 --- /dev/null +++ b/280_anvio/prodigal-2.6.3-20230127-GCCcore-12.3.0.eb @@ -0,0 +1,47 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Updated: Pavel Grochal (INUITS) +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'prodigal' +local_commit = 'c1e2d36' +version = '2.6.3-20230127' + +homepage = 'https://github.com/hyattpd/Prodigal/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['5b4ac9f99038b143c62f4d86d3f77bc801f64daca04c26ba9789bf0a64904ac9'] + +builddependencies = [('binutils', '2.40')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +sanity_check_commands = ["prodigal -h"] + +moduleclass = 'bio' diff --git a/280_anvio/statsmodels-0.14.1-gfbf-2023a.eb b/280_anvio/statsmodels-0.14.1-gfbf-2023a.eb new file mode 100644 index 00000000..6c62326b --- /dev/null +++ b/280_anvio/statsmodels-0.14.1-gfbf-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.14.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.6', { + 'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'], + }), + (name, version, { + 'checksums': ['2260efdc1ef89f39c670a0bd8151b1d0843567781bcafec6cda0534eb47a94f6'], + 'preinstallopts': """sed -i 's/name=DISTNAME/name=DISTNAME, version = "%(version)s"/g' setup.py && """, + }), +] + +moduleclass = 'math'