GNU bug report logs - #38674
[PATCH] gnu: tophat: Build with GCC 5

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <guix-patches <at> gnu.org>
Cc: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Subject: [PATCH] gnu: tophat: Build with GCC 5
Date: Thu, 19 Dec 2019 19:53:31 +0100

* 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 <at> systemreboot.net>
 ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua <at> nextjournal.com>
 ;;; Copyright © 2018 Gábor Boskovits <boskovits <at> gmail.com>
-;;; Copyright © 2018 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
+;;; Copyright © 2018, 2019 Mădălin Ionel Patrașcu <madalinionel.patrascu <at> mdc-berlin.de>
 ;;; Copyright © 2019 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
 ;;; Copyright © 2019 Brian Leung <bkleung89 <at> 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

Message #10 received at 38674-done <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
Cc: 38674-done <at> debbugs.gnu.org
Subject: Re: [bug#38674] [PATCH] gnu: tophat: Build with GCC 5
Date: Mon, 23 Dec 2019 19:32:05 +0100

Hi,

Mădălin Ionel Patrașcu <madalinionel.patrascu <at> 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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