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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>
master
Mădălin Ionel Patrașcu 2019-12-19 19:53:31 +01:00 committed by Ludovic Courtès
parent 92d2205a19
commit 3bedd9f40f
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1 changed files with 9 additions and 7 deletions
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16
gnu/packages/bioinformatics.scm
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@ -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