diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2020-08-12 21:55:06 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2020-08-12 21:55:06 +0200 |
| commit | bcdc61bfa1b4800f19c985dd73ad2d5a696e5307 (patch) | |
| tree | 4eb6f2478345747be92611e50968c18fccbfa459 /gnu | |
| parent | c9a16728410f11f4bd9b49632ca2b13df849ecdc (diff) | |
gnu: tophat: Hide default GCC.
* gnu/packages/bioinformatics.scm (tophat)[arguments]: Add build phase
"hide-default-gcc".
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 13 |
1 files changed, 12 insertions, 1 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 57bfcf8207..2f4a2b1461 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) |