Browse Source

gnu: Add gffcompare.

gnu/packages/bioinformatics.scm (gffcompare): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
wip-ipfs
pimi 4 years ago
committed by Leo Famulari
parent
commit
4f9355c360
No known key found for this signature in database GPG Key ID: 2646FA30BACA7F08
  1. 64
      gnu/packages/bioinformatics.scm

64
gnu/packages/bioinformatics.scm

@ -11,6 +11,7 @@
;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net>
;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com>
;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com>
;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
;;;
;;; This file is part of GNU Guix.
;;;
@ -13494,3 +13495,66 @@ pseudotime and trajectory inference and differential expression testing. The
Python-based implementation efficiently deals with datasets of more than one
million cells.")
(license license:bsd-3)))
(define-public gffcompare
(let ((commit "be56ef4349ea3966c12c6397f85e49e047361c41")
(revision "1"))
(package
(name "gffcompare")
(version (git-version "0.10.15" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gpertea/gffcompare/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0cp5qpxdhw4mxpya5dld8wi3jk00zyklm6rcri426wydinrnfmkg"))))
(build-system gnu-build-system)
(arguments
`(#:tests? #f ; no check target
#:phases
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'copy-gclib-source
(lambda* (#:key inputs #:allow-other-keys)
(mkdir "../gclib")
(copy-recursively
(assoc-ref inputs "gclib-source") "../gclib")
#t))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(install-file "gffcompare" bin)
#t))))))
(native-inputs
`(("gclib-source" ; see 'README.md' of gffcompare
,(let ((commit "54917d0849c1e83cfb057b5f712e5cb6a35d948f")
(revision "1")
(name "gclib")
(version (git-version "0.10.3" revision commit)))
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/gpertea/gclib/")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32 "0b51lc0b8syrv7186fd7n8f15rwnf264qgfmm2palrwks1px24mr")))))))
(home-page "https://github.com/gpertea/gffcompare/")
(synopsis "Tool for comparing or classifing transcripts of RNA-Seq")
(description
"@code{gffcompare} is a tool that can:
@enumerate
@item compare and evaluate the accuracy of RNA-Seq transcript assemblers
(Cufflinks, Stringtie);
@item collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g.
resulted from assembly of different samples);
@item classify transcripts from one or multiple GTF/GFF3 files as they relate to
reference transcripts provided in a annotation file (also in GTF/GFF3 format).
@end enumerate")
(license
(list
license:expat ;license for gffcompare
license:artistic2.0))))) ;license for gclib

Loading…
Cancel
Save