diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 81 |
1 files changed, 37 insertions, 44 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 92a299634f..db378d791d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -5,7 +5,7 @@ ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016, 2020, 2021 Roel Janssen <roel@gnu.org> ;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> -;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com> +;;; Copyright © 2016, 2020, 2022 Marius Bakke <marius@gnu.org> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017, 2021 Arun Isaac <arunisaac@systemreboot.net> @@ -14620,55 +14620,48 @@ alignments, trees and genomic annotations.") (license license:bsd-3))) (define-public python-gffutils - ;; The latest release is older more than a year than the latest commit - (let ((commit "4034c54600813b1402945e12faa91b3a53162cf1") - (revision "1")) - (package - (name "python-gffutils") - (version (git-version "0.9" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/daler/gffutils") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1rwafjdnbir5wnk0ap06ww4lra3p5frhy7mfs03rlldgfnwxymsn")))) - (build-system python-build-system) - (arguments - `(#:phases - (modify-phases %standard-phases - (replace 'check - (lambda _ + (package + (name "python-gffutils") + (version "0.10.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/daler/gffutils") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1gkzk7ps6w3ai2r81js9s9bzpba0jmxychnd2da6n9ggdnf2xzqz")))) + (build-system python-build-system) + (arguments + '(#:phases + (modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? ;; Tests need to access the HOME directory (setenv "HOME" "/tmp") - (invoke "nosetests" "-a" "!slow"))) - (add-after 'unpack 'make-gz-files-writable - (lambda _ - (for-each make-file-writable - (find-files "." "\\.gz")) - #t))))) - (propagated-inputs - (list python-argcomplete - python-argh - python-biopython - python-pybedtools - python-pyfaidx - python-simplejson - python-six)) - (native-inputs - (list python-nose)) - (home-page "https://github.com/daler/gffutils") - (synopsis "Tool for manipulation of GFF and GTF files") - (description - "python-gffutils is a Python package for working with and manipulating + (invoke "nosetests" "-a" "!slow"))))))) + (propagated-inputs + (list python-argcomplete + python-argh + python-biopython + python-pybedtools + python-pyfaidx + python-simplejson + python-six)) + (native-inputs + (list python-nose)) + (home-page "https://github.com/daler/gffutils") + (synopsis "Tool for manipulation of GFF and GTF files") + (description + "python-gffutils is a Python package for working with and manipulating the GFF and GTF format files typically used for genomic annotations. The files are loaded into a SQLite database, allowing much more complex manipulation of hierarchical features (e.g., genes, transcripts, and exons) than is possible with plain-text methods alone.") - (license license:expat)))) + (license license:expat))) (define-public indelfixer (package |