diff --git a/235_singleM/SingleM-0.16.0-foss-2023a.eb b/235_singleM/SingleM-0.16.0-foss-2023a.eb index 45bdfc2b..25fc18b7 100644 --- a/235_singleM/SingleM-0.16.0-foss-2023a.eb +++ b/235_singleM/SingleM-0.16.0-foss-2023a.eb @@ -11,53 +11,15 @@ finding bias in genome recovery, computing ecological diversity metrics, and lin toolchain = {'name': 'foss', 'version': '2023a'} -# DEPS - # OK - python>=3.7 #, <3.10 # https://github.com/google-research/google-research/issues/779 means scann (at least 1.2.8) fails to install via pip for 3.10. Older python versions than 3.7 may also work, not tested. - # OK - diamond>=2.1.7 # Getting segmentation fault on test_insert_prefilter otherwise - # OK - biopython - # OK - hmmer - # OK - orfm - # OK - mfqe - # ok - extern - # ok - graftm>=0.15.0 # Version needed for --translation-table - # OK - krona - # OK - pplacer - # OK - sra-tools - # OK - ncbi-ngs-sdk - in SRA-Toolkit - # OK - sqlite - in python - # ok - squarify - # OK - mafft - # OK - seqmagick - # OK - expressbetadiversity - # OK - cd-hit -> created - # OK - fasttree - # ok - fastalite - # OK - jinja2 - pypi bundle - # OK - pip - # OK - sqlalchemy - # OK - pandas - # ok - bird_tool_utils_python>=0.4.1 - # ok - zenodo_backpack - # OK - smafa>=0.7.0 -> created - # ok - pyranges - # OK - polars>=0.19.3 # supplement with taxon genome length requires this, for strip_chars - # OK - prodigal - # OK - tqdm - # OK - pyarrow - # # - galah >= 0.4.0 # 0.4.0 is the first version with checkm2 quality inputs, but not yet released - # - pytest # For testing only - # - ipython # For testing only - # - sqlparse # Don't understand why, but this isn't being installed before tests are run on GH actions. Required indirectly (by taxtastic). - +builddependencies = [('hatchling', '1.18.0')] dependencies = [ - ('Python', '3.11.3'), # with SQLite + ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), - ('SciPy-bundle', '2023.07'), # for pandas - # ('matplotlib', '3.7.2'), - ('Biopython', '1.83'), - ('polars', '0.20.2'), # polars >= 0.19.3 + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('polars', '0.20.2'), ('tqdm', '4.66.1'), - ('Arrow', '14.0.1'), # for pyarrow + ('Arrow', '14.0.1'), ('DIAMOND', '2.1.8'), ('HMMER', '3.4'), ('MAFFT', '7.520', '-with-extensions'), @@ -73,18 +35,39 @@ dependencies = [ ('CD-HIT', '4.8.1'), ('smafa', '0.8.0'), ('prodigal', '2.6.3'), - # - # ('DendroPy', '4.4.0'), - # ('PyYAML', '5.1'), - # ('PostgreSQL', '11.3', versionsuffix), # required for psycopg2 - # ('VSEARCH', '2.13.4'), - # ('fxtract', '2.3'), + ('biom-format', '2.1.15'), + ('DendroPy', '4.6.1'), + ('PyYAML', '6.0'), + ('psycopg', '3.2.1'), ] use_pip = True sanity_pip_check = True exts_list = [ + ('psycopg2-binary', '2.9.9', { + 'modulename': 'psycopg2', + 'checksums': ['7f01846810177d829c7692f1f5ada8096762d9172af1b1a28d4ab5b77c923c1c'], + }), + ('sqlparse', '0.5.1', { + 'checksums': ['bb6b4df465655ef332548e24f08e205afc81b9ab86cb1c45657a7ff173a3a00e'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('argparse-manpage-birdtools', '1.7.0', { + 'modulename': 'build_manpages', + 'checksums': ['20eae3079a4a2dbe1a7557ef7276a4d8e5a44c7c4223afb50f4f1d0ae0e7d103'], + }), + ('taxtastic', '0.10.0', { + 'checksums': ['32db30aa2e499fbae913b991cd087fa69684ac4ff934b957c30b6085866f1748'], + }), ('zenodo_backpack', '0.3.1', { 'checksums': ['dc91f3c427f976465789746e94736abfa536cf42dc2e49b6d6067382a9a39b26'], }), diff --git a/235_singleM/SingleM_pre_PR.eb b/235_singleM/SingleM_pre_PR.eb new file mode 100644 index 00000000..ebffd432 --- /dev/null +++ b/235_singleM/SingleM_pre_PR.eb @@ -0,0 +1,159 @@ +easyblock = 'PythonBundle' + +name = 'SingleM' +version = '0.16.0' + +homepage = 'https://github.com/wwood/singlem' +description = """SingleM is a tool for profiling shotgun metagenomes. +It has a particular strength in detecting microbial lineages which are not in reference databases. +The method it uses also makes it suitable for some related tasks, such as assessing eukaryotic contamination, +finding bias in genome recovery, computing ecological diversity metrics, and lineage-targeted MAG recovery.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +# DEPS + # OK - python>=3.7 #, <3.10 # https://github.com/google-research/google-research/issues/779 means scann (at least 1.2.8) fails to install via pip for 3.10. Older python versions than 3.7 may also work, not tested. + # OK - diamond>=2.1.7 # Getting segmentation fault on test_insert_prefilter otherwise + # OK - biopython + # OK - hmmer + # OK - orfm + # OK - mfqe + # ok - extern + # ok - graftm>=0.15.0 # Version needed for --translation-table + # OK - krona + # OK - pplacer + # OK - sra-tools + # OK - ncbi-ngs-sdk - in SRA-Toolkit + # OK - sqlite - in python + # ok - squarify + # OK - mafft + # OK - seqmagick + # OK - expressbetadiversity + # OK - cd-hit -> created + # OK - fasttree + # ok - fastalite + # OK - jinja2 - pypi bundle + # OK - pip + # OK - sqlalchemy + # OK - pandas + # ok - bird_tool_utils_python>=0.4.1 + # ok - zenodo_backpack + # OK - smafa>=0.7.0 -> created + # ok - pyranges + # OK - polars>=0.19.3 # supplement with taxon genome length requires this, for strip_chars + # OK - prodigal + # OK - tqdm + # OK - pyarrow + # # - galah >= 0.4.0 # 0.4.0 is the first version with checkm2 quality inputs, but not yet released + # - pytest # For testing only + # - ipython # For testing only + # - sqlparse # Don't understand why, but this isn't being installed before tests are run on GH actions. Required indirectly (by taxtastic). + # graftm 0.15.1 requires biom-format, OK + # graftm 0.15.1 requires dendropy, OK + # graftm 0.15.1 requires pyyaml, OK + # graftm 0.15.1 requires taxtastic, ok + # bird-tool-utils 0.4.1 requires argparse-manpage-birdtools, ok + # pyranges 0.0.129 requires natsort, ok + # pyranges 0.0.129 requires ncls, ok + # pyranges 0.0.129 requires sorted-nearest, ok + # taxtastic 0.10.0 requires psycopg, created OK + # taxtastic 0.10.0 requires psycopg2-binary, ok exts - not same as psycopg2 in EB + # taxtastic 0.10.0 requires sqlparse, ok + +builddependencies = [('hatchling', '1.18.0')] +dependencies = [ + ('Python', '3.11.3'), # with SQLite + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), # for pandas + # ('matplotlib', '3.7.2'), + ('Biopython', '1.83'), + ('polars', '0.20.2'), # polars >= 0.19.3 + ('tqdm', '4.66.1'), + ('Arrow', '14.0.1'), # for pyarrow + ('DIAMOND', '2.1.8'), + ('HMMER', '3.4'), + ('MAFFT', '7.520', '-with-extensions'), + ('OrfM', '0.7.1'), + ('mfqe', '0.5.0'), + ('KronaTools', '2.8.1'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('SRA-Toolkit', '3.0.10'), + ('Seqmagick', '0.8.6'), + ('ExpressBetaDiversity', '1.0.10'), + ('FastTree', '2.1.11'), + ('SQLAlchemy', '2.0.25'), + ('CD-HIT', '4.8.1'), + ('smafa', '0.8.0'), + ('prodigal', '2.6.3'), + ('biom-format', '2.1.15'), + ('DendroPy', '4.6.1'), + ('PyYAML', '6.0'), + ('psycopg', '3.2.1'), + # ('VSEARCH', '2.13.4'), + # ('fxtract', '2.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('psycopg2-binary', '2.9.9', { + 'modulename': 'psycopg2', + 'checksums': ['7f01846810177d829c7692f1f5ada8096762d9172af1b1a28d4ab5b77c923c1c'], + }), + ('sqlparse', '0.5.1', { + 'checksums': ['bb6b4df465655ef332548e24f08e205afc81b9ab86cb1c45657a7ff173a3a00e'], + }), + ('sorted_nearest', '0.0.39', { + 'checksums': ['16a51d5db87ae226b47ace43c176bb672477a1b7ba8052ea9291a6356c9c69b1'], + }), + ('ncls', '0.0.68', { + 'checksums': ['81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('argparse-manpage-birdtools', '1.7.0', { + 'modulename': 'build_manpages', + 'checksums': ['20eae3079a4a2dbe1a7557ef7276a4d8e5a44c7c4223afb50f4f1d0ae0e7d103'], + }), + ('taxtastic', '0.10.0', { + 'checksums': ['32db30aa2e499fbae913b991cd087fa69684ac4ff934b957c30b6085866f1748'], + }), + ('zenodo_backpack', '0.3.1', { + 'checksums': ['dc91f3c427f976465789746e94736abfa536cf42dc2e49b6d6067382a9a39b26'], + }), + ('bird_tool_utils', '0.4.1', { + 'checksums': ['6fe80f9608626427e8d382c5341c24088d61f17336fb6ce834d40aa4577499b5'], + }), + ('fastalite', '0.4.1', { + 'checksums': ['e85413ee22bdb3fe0f73f5226771cf71eb33074ccdf8bbefff3a1bc6242de37c'], + }), + ('squarify', '0.4.3', { + 'checksums': ['54091f6ad175f7f201f8934574e647ce1b50dedc478c5fd968688eb7d7469f95'], + }), + ('pyranges', '0.0.129', { + 'checksums': ['bee83b4fad0062be9586668c6b0fc4270d5e761951975e018202993680071fb3'], + }), + ('extern', '0.4.1', { + 'checksums': ['0ff01adc2ad423f3d1e31641024b3974569fb0127b4d925bc6bed1cb86b6b1e4'], + }), + ('graftm', '0.15.1', { + 'checksums': ['80d828c311d2d6067977cfad5b6bac7cbc5d223ef8ab770d676b39bf2bc75163'], + }), + ('singlem', version, { + 'checksums': ['64e43a6a40795d68ff5aed7dfff9a94532b862f25a28c27de7d588d64a8c7f79'], + }), +] + +sanity_check_paths = { + 'files': ['bin/graftM', 'bin/singlem'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "graftM --help", + "singlem --help", +] + +moduleclass = 'bio' diff --git a/235_singleM/psycopg.eb b/235_singleM/psycopg.eb new file mode 100644 index 00000000..5c0aab8a --- /dev/null +++ b/235_singleM/psycopg.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psycopg' +version = '3.2.1' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('PostgreSQL', '16.1'), +] + +exts_list = [ + (name, version, { + 'checksums': ['dc8da6dc8729dacacda3cc2f17d2c9397a70a66cf0d2b69c91065d60d5f00cb7'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib'