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bh=vDeVhxYH/fAYIi+Ic8c68uXucMckTwxRf0T9WAtv6A0=; b=Ak6GKLFUEksG6UNtxwebLYWiSZ7j7dSUAdYfeC5WgLxPF4A1IlPcPxEY6xEoWbTz4j+83T 5ZEnNFbI8sLyquHqao9R0q3U8QsMvzcjudDwkiZHaqhWqb2qLiucdAxcm3Ce1Y/WGiop2K +SQZI4BuCP/kNX5QwuqjRNTzOW/1nxC+88AUpU8MZYNTYrZ+lMap2gazEUlEQem62wfz6U QPWDH+y+WCatn9rLzMd4aYNzd0evuFLOFJS9EDCa1y8rKD1HoG7h6YwtD/ujAHmU11rwxn VfAmvUJ1glfD/an3WVOadnXbI5ArDQ49VXAS3f3wyjvqWWRMze4imULn+hvC5A== X-Migadu-Scanner: scn1.migadu.com Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=mdc-berlin.de header.s=mdc header.b=VlfjGfZd; dmarc=fail reason="SPF not aligned (relaxed)" header.from=mdc-berlin.de (policy=none); spf=pass (aspmx1.migadu.com: domain of "guix-patches-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-patches-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.92 X-Spam-Score: 6.92 X-Migadu-Queue-Id: D35F33A33D X-TUID: 8NGyoA+7d+4Q * gnu/packages/bioinformatics.scm (python-mgatk): New variable. --- gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++++++++++++ 1 file changed, 52 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index afca5ab93b..abb7cf374a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -12628,6 +12628,58 @@ (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)) + (sha256 + (base32 "19iklfv1brwsfg1l5lrs3z8m343nskkn1998c1fs7fdn0lgrki2p")))) + (build-system python-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? + ;; This test is based on the md5 module + (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-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") base-commit: d07342b16612cfdffad6a7b3504b74e0d95d551f -- 2.39.2