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Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 53 |
1 files changed, 53 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index c629b79c39..b0736d32e4 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13177,6 +13177,59 @@ similar genomes and choosing the best representative genome for each genome set.") (license license:expat))) +(define-public instrain + (package + (name "instrain") + (version "1.5.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "inStrain" version)) + (sha256 + (base32 + "0ykqlpf6yz4caihsaz3ys00cyvlr7wdj4s9a8rh56q5r8xf80ic0")))) + (build-system python-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-relative-imports + (lambda _ + (substitute* "docker/run_instrain.py" + (("from s3_utils") + "from .s3_utils") + (("from job_utils") + "from .job_utils"))))))) + (inputs + `(("python-biopython" ,python-biopython) + ("python-boto3" ,python-boto3) + ("python-h5py" ,python-h5py) + ("python-lmfit" ,python-lmfit) + ("python-matplotlib" ,python-matplotlib) + ("python-networkx" ,python-networkx) + ("python-numba" ,python-numba) + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python-psutil" ,python-psutil) + ("python-pysam" ,python-pysam) + ("python-scikit-learn" ,python-scikit-learn) + ("python-seaborn" ,python-seaborn) + ("python-tqdm" ,python-tqdm) + ;; drep is needed for deprecated plot utilities + ("python-drep" ,python-drep))) + (native-inputs + `(("python-pytest" ,python-pytest))) + (home-page "https://github.com/MrOlm/inStrain") + (synopsis "Calculation of strain-level metrics") + (description + "inStrain is a Python program for analysis of co-occurring genome +populations from metagenomes that allows highly accurate genome comparisons, +analysis of coverage, microdiversity, and linkage, and sensitive SNP detection +with gene localization and synonymous non-synonymous identification.") + ;; The tool itself says that the license is "MIT", but the repository + ;; contains a LICENSE file with the GPLv3. + ;; See https://github.com/MrOlm/inStrain/issues/51 + (license license:expat))) + (define-public gffcompare (let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41") (revision "1")) |