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branch master updated: gnu: tophat: Hide default GCC.
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guix-commits |
Subject: |
branch master updated: gnu: tophat: Hide default GCC. |
Date: |
Wed, 12 Aug 2020 15:55:52 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new bcdc61b gnu: tophat: Hide default GCC.
bcdc61b is described below
commit bcdc61bfa1b4800f19c985dd73ad2d5a696e5307
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Aug 12 21:55:06 2020 +0200
gnu: tophat: Hide default GCC.
* gnu/packages/bioinformatics.scm (tophat)[arguments]: Add build phase
"hide-default-gcc".
---
gnu/packages/bioinformatics.scm | 13 ++++++++++++-
1 file changed, 12 insertions(+), 1 deletion(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 57bfcf8..2f4a2b1 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1683,6 +1683,17 @@ genome (2.9 GB for paired-end).")
'(#:parallel-build? #f ; not supported
#:phases
(modify-phases %standard-phases
+ (add-after 'set-paths 'hide-default-gcc
+ (lambda* (#:key inputs #:allow-other-keys)
+ (let ((gcc (assoc-ref inputs "gcc")))
+ ;; Remove the default GCC from CPLUS_INCLUDE_PATH to prevent
+ ;; conflicts with the GCC 5 input.
+ (setenv "CPLUS_INCLUDE_PATH"
+ (string-join
+ (delete (string-append gcc "/include/c++")
+ (string-split (getenv "CPLUS_INCLUDE_PATH")
#\:))
+ ":"))
+ #t)))
(add-after 'unpack 'use-system-samtools
(lambda* (#:key inputs #:allow-other-keys)
(substitute* "src/Makefile.in"
@@ -1705,7 +1716,7 @@ genome (2.9 GB for paired-end).")
(("#include <sam.h>") "#include <samtools/sam.h>"))
#t)))))
(native-inputs
- `(("gcc" ,gcc-5))) ;; doesn't build with later versions
+ `(("gcc@5" ,gcc-5))) ;; doesn't build with later versions
(inputs
`(("boost" ,boost)
("bowtie" ,bowtie)
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