@@ -12628,6 +12628,60 @@ (define-public python-biothings-client
API services.")
(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")