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authorMădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>2019-12-16 16:25:19 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-12-16 23:27:00 +0100
commitcfd83f3282ed1c416e0e99bdfc334d9be0d1856b (patch)
tree1305090082ebcf663c9b55a4e63b6de2985c2bf3 /gnu
parentb7716f1b39b596f74fe0f41009ef506d242c5ece (diff)
downloadpatches-cfd83f3282ed1c416e0e99bdfc334d9be0d1856b.tar
patches-cfd83f3282ed1c416e0e99bdfc334d9be0d1856b.tar.gz
gnu: Add python-gffutils.
* gnu/packages/bioinformatics.scm (python-gffutils): New variable. Co-authored-by: Ricardo Wurmus <rekado@elephly.net>
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm51
1 files changed, 51 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index eb2d6f1be3..7bbdcae149 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -15384,3 +15384,54 @@ methylation metrics from them. MethylDackel requires an indexed fasta file
containing the reference genome as well.")
;; See https://github.com/dpryan79/MethylDackel/issues/85
(license license:expat)))
+
+(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.git")
+ (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 _
+ ;; 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
+ `(("python-argcomplete" ,python-argcomplete)
+ ("python-argh" ,python-argh)
+ ("python-biopython" ,python-biopython)
+ ("python-pybedtools" ,python-pybedtools)
+ ("python-pyfaidx" ,python-pyfaidx)
+ ("python-simplejson" ,python-simplejson)
+ ("python-six" ,python-six)))
+ (native-inputs
+ `(("python-nose" , 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 sqlite3 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)))) ;; MIT license