* [bug#38674] [PATCH] gnu: tophat: Build with GCC 5
@ 2019-12-19 18:53 Mădălin Ionel Patrașcu
2019-12-23 18:32 ` bug#38674: " Ludovic Courtès
0 siblings, 1 reply; 2+ messages in thread
From: Mădălin Ionel Patrașcu @ 2019-12-19 18:53 UTC (permalink / raw)
To: 38674; +Cc: Mădălin Ionel Patrașcu
* 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(-)
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
--
2.24.1
^ permalink raw reply related [flat|nested] 2+ messages in thread
* bug#38674: [PATCH] gnu: tophat: Build with GCC 5
2019-12-19 18:53 [bug#38674] [PATCH] gnu: tophat: Build with GCC 5 Mădălin Ionel Patrașcu
@ 2019-12-23 18:32 ` Ludovic Courtès
0 siblings, 0 replies; 2+ messages in thread
From: Ludovic Courtès @ 2019-12-23 18:32 UTC (permalink / raw)
To: Mădălin Ionel Patrașcu; +Cc: 38674-done
Hi,
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> skribis:
> * gnu/packages/python-xyz.scm (tophat)[native-inputs]: Add gcc-5.
> (tophat)[inputs]: Reorder alphabetically the dependencies.
> (tophat)[home-page]: Swapp to https.
Applied, thanks!
Ludo’.
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2019-12-19 18:53 [bug#38674] [PATCH] gnu: tophat: Build with GCC 5 Mădălin Ionel Patrașcu
2019-12-23 18:32 ` bug#38674: " Ludovic Courtès
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