diff options
| author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2023-05-12 12:43:03 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-05-12 15:30:44 +0200 |
| commit | 263f235cd0a2955e865fe38036f84c2bf34375ff (patch) | |
| tree | 4c503c04742b9244fb8c49bfb339dee7ddfb301e /gnu/packages/bioinformatics.scm | |
| parent | 40310efde9b4a4f2cf98081d6cd10f843685ebb6 (diff) | |
gnu: Add python-mgatk.
* gnu/packages/bioinformatics.scm (python-mgatk): New variable.
Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 50 |
1 files changed, 50 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index afca5ab93b..500c418b13 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12628,6 +12628,56 @@ single-cell RNA-seq data.") API services.") (license license:bsd-3))) +(define-public python-mgatk + (package + (name "python-mgatk") + (version "0.6.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/caleblareau/mgatk") + ;; There is no tag for 0.6.7, but this is the commit + ;; corresponding to the version bump. + (commit "2633903acb1fb406bb58c787f320c3641f446ee7"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "19iklfv1brwsfg1l5lrs3z8m343nskkn1998c1fs7fdn0lgrki2p")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; The md5 module has been removed in Python 3 + (add-after 'unpack 'python3-compatibility + (lambda _ + (substitute* "tests/test_cli.py" + (("import md5") "from hashlib import md5") + (("md5.new") "md5") + (("\\.digest") ".hexdigest"))))))) + (propagated-inputs + (list python-biopython + python-click + python-numpy + python-optparse-pretty + python-pandas + python-pysam + python-regex + python-ruamel.yaml + snakemake)) + (native-inputs + (list python-pytest)) + (home-page "https://github.com/caleblareau/mgatk") + (synopsis "Mitochondrial genome analysis toolkit.") + (description "This package is a Python-based command line interface for +processing .bam files with mitochondrial reads and generating high-quality +heteroplasmy estimation from sequencing data. The mgatk package places a +special emphasis on mitochondrial genotypes generated from single-cell +genomics data, primarily @acronym{mtscATAC-seq, mitochondrial single-cell +ATAC-sequence}, but is generally applicable across other assays.") + (license license:expat))) + (define-public python-multivelo (package (name "python-multivelo") |