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gnu: python-gffutils: Update to 0.10.1.

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* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1.
[arguments]: Remove obsolete phase.  Respect TESTS? in check phase while at
it.
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Marius Bakke 2022-02-15 00:14:16 +01:00
parent 48daa39724
commit b5d472ef5d
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1 changed files with 37 additions and 44 deletions
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gnu/packages/bioinformatics.scm
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@ -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 @@ (define-public phast
(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