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| -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 c2e9f209bc..1bc451715c 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -25,6 +25,7 @@ ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net> ;;; Copyright © 2022, 2023 Navid Afkhami <navid.afkhami@mdc-berlin.de> ;;; Copyright © 2022 Antero Mejr <antero@mailbox.org> +;;; Copyright © 2024 Alexis Simon <alexis.simon@runbox.com> ;;; ;;; This file is part of GNU Guix. ;;; @@ -1916,6 +1917,58 @@ from high-throughput single-cell RNA sequencing (scRNA-seq) data.") and sequence consensus.") (license license:expat))) +(define-public python-cyvcf2 + (package + (name "python-cyvcf2") + (version "0.30.28") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/brentp/cyvcf2") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "16yhfax509zyip8kkq2b0lflx5bdq5why7d785ayrqyzzq2rxqkk")) + (modules '((guix build utils))) + (snippet + ;; Delete bundled library + '(delete-file-recursively "htslib")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python" "setup.py" "build_ext" "--inplace"))) + (add-after 'unpack 'fix-setup + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "setup.py" + (("^htslib_include_dirs =.*") + (string-append "htslib_include_dirs = [\"" + #$(this-package-input "htslib") "/include\"]\n")) + (("lib_name = \"libhts.so\"") + (string-append "lib_name = \"" + (search-input-file inputs "lib/libhts.so.3") + "\"\n"))))) + (add-before 'build 'use-system-htslib-package + (lambda _ + (setenv "CYTHONIZE" "1") + (setenv "CYVCF2_HTSLIB_MODE" "EXTERNAL")))))) + (inputs (list curl htslib libdeflate openssl zlib)) + (native-inputs (list python-cython python-pytest)) + (propagated-inputs + (list python-click + python-coloredlogs + python-numpy)) + (home-page "https://github.com/brentp/cyvcf2/") + (synopsis "Fast vcf file parsing with Cython and htslib") + (description "Cyvcf2 is a Cython wrapper around htslib built for fast +parsing of Variant Call Format (VCF) files.") + (license license:expat))) + (define-public python-decoupler-py ;; This latest commit fixes a bug in test_omnip.py. (let ((commit "459b235348ddd9135217a3722d9dd1caa9a14ace") |