Mădălin Ionel Patrașcu wrote 5 years ago
(address . guix-patches@gnu.org)(name . Mădălin Ionel Patrașcu)(address . madalinionel.patrascu@mdc-berlin.de)
20191219185331.19702-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5.
(tophat)[inputs]: Reorder alphabetically the dependencies.
(tophat)[home-page]: Swapp to https.
---
gnu/packages/bioinformatics.scm | 16 +++++++++-------
1 file changed, 9 insertions(+), 7 deletions(-)
Toggle diff (48 lines)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 528b603476..0f6c120687 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
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