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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,159 @@ | ||
| easyblock = 'PythonBundle' | ||
|
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| name = 'SingleM' | ||
| version = '0.16.0' | ||
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| 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.""" | ||
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| toolchain = {'name': 'foss', 'version': '2023a'} | ||
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| # 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 | ||
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| 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'), | ||
| ] | ||
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| use_pip = True | ||
| sanity_pip_check = True | ||
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| 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'], | ||
| }), | ||
| ] | ||
|
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| sanity_check_paths = { | ||
| 'files': ['bin/graftM', 'bin/singlem'], | ||
| 'dirs': ['lib/python%(pyshortver)s/site-packages'], | ||
| } | ||
|
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| sanity_check_commands = [ | ||
| "graftM --help", | ||
| "singlem --help", | ||
| ] | ||
|
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| moduleclass = 'bio' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,26 @@ | ||
| easyblock = 'PythonBundle' | ||
|
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| name = 'psycopg' | ||
| version = '3.2.1' | ||
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| homepage = 'https://psycopg.org/' | ||
| description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." | ||
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| toolchain = {'name': 'GCCcore', 'version': '12.3.0'} | ||
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| builddependencies = [('binutils', '2.40')] | ||
| dependencies = [ | ||
| ('Python', '3.11.3'), | ||
| ('PostgreSQL', '16.1'), | ||
| ] | ||
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| exts_list = [ | ||
| (name, version, { | ||
| 'checksums': ['dc8da6dc8729dacacda3cc2f17d2c9397a70a66cf0d2b69c91065d60d5f00cb7'], | ||
| }), | ||
| ] | ||
|
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| use_pip = True | ||
| sanity_pip_check = True | ||
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| moduleclass = 'lib' |