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Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 64 |
1 files changed, 64 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3c300e48e9..22a00894c2 100644 --- a/gnu/packages/bioinformatics.scm +++ b/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 |