summaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorMarius Bakke <marius@gnu.org>2022-02-15 00:14:16 +0100
committerMarius Bakke <marius@gnu.org>2022-02-15 00:21:16 +0100
commitb5d472ef5d5c5e36126d5d949dc0b8d7c7610142 (patch)
tree3993114d4c8bcf126ec260f90ae6e9873bb47cf1
parent48daa39724487607f07c192e47a18834f1e65182 (diff)
gnu: python-gffutils: Update to 0.10.1.
* gnu/packages/bioinformatics.scm (python-gffutils): Update to 0.10.1. [arguments]: Remove obsolete phase. Respect TESTS? in check phase while at it.
-rw-r--r--gnu/packages/bioinformatics.scm81
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