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(license license:bsd-3))) +(define-public python-mgatk + (let ((commit "2633903acb1fb406bb58c787f320c3641f446ee7") + (revision "0")) + (package + (name "python-mgatk") + (version "0.6.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/caleblareau/mgatk") + (commit commit))) + (file-name (git-file-name name version)) + ;(method url-fetch) + ;(uri (pypi-uri "mgatk" version)) + (sha256 + (base32 "19iklfv1brwsfg1l5lrs3z8m343nskkn1998c1fs7fdn0lgrki2p")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + ;; The md5 module has beed deprecated since Python 2.5 + (add-after 'unpack 'make-python3-compatible + (lambda* _ + (substitute* "tests/test_cli.py" + (("import md5") "")))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "-k" "not file_checksums_equal"))))))) + (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-minimal + 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")