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| author | Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> | 2019-12-19 19:53:31 +0100 |
|---|---|---|
| committer | Ludovic Courtès <ludo@gnu.org> | 2019-12-23 19:38:14 +0100 |
| commit | 3bedd9f40f32a01357db642c4ea5738e1299da2c (patch) | |
| tree | a071969462d7fd2c9af23a6cd190fbb0fad3686c /gnu/packages/bioinformatics.scm | |
| parent | 92d2205a19e9abc040fc245859613a4a582a8dcb (diff) | |
| download | patches-3bedd9f40f32a01357db642c4ea5738e1299da2c.tar patches-3bedd9f40f32a01357db642c4ea5738e1299da2c.tar.gz | |
gnu: tophat: Build with GCC 5
* gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5.
(tophat)[inputs]: Reorder alphabetically the dependencies.
(tophat)[home-page]: Swapp to https.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 16 |
1 files changed, 9 insertions, 7 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 52330cb4c1..6488642df8 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11,7 +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> +;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> ;;; @@ -1615,7 +1615,7 @@ genome (2.9 GB for paired-end).") #t)))) (build-system gnu-build-system) (arguments - '(#:parallel-build? #f ; not supported + '(#:parallel-build? #f ; not supported #:phases (modify-phases %standard-phases (add-after 'unpack 'use-system-samtools @@ -1639,16 +1639,18 @@ genome (2.9 GB for paired-end).") (("#include <bam.h>") "#include <samtools/bam.h>") (("#include <sam.h>") "#include <samtools/sam.h>")) #t))))) + (native-inputs + `(("gcc" ,gcc-5))) ;; doesn't build with later versions (inputs `(("boost" ,boost) ("bowtie" ,bowtie) - ("samtools" ,samtools-0.1) ("ncurses" ,ncurses) - ("python" ,python-2) ("perl" ,perl) - ("zlib" ,zlib) - ("seqan" ,seqan-1))) - (home-page "http://ccb.jhu.edu/software/tophat/index.shtml") + ("python" ,python-2) + ("samtools" ,samtools-0.1) + ("seqan" ,seqan-1) + ("zlib" ,zlib))) + (home-page "https://ccb.jhu.edu/software/tophat/index.shtml") (synopsis "Spliced read mapper for RNA-Seq data") (description "TopHat is a fast splice junction mapper for nucleotide sequence |