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gnu: tophat: Hide default GCC.

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* gnu/packages/bioinformatics.scm (tophat)[arguments]: Add build phase
"hide-default-gcc".
This commit is contained in:
Ricardo Wurmus 2020-08-12 21:55:06 +02:00
parent c9a1672841
commit bcdc61bfa1
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1 changed files with 12 additions and 1 deletions
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gnu/packages/bioinformatics.scm
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@ -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)