From bcdc61bfa1b4800f19c985dd73ad2d5a696e5307 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Wed, 12 Aug 2020 21:55:06 +0200 Subject: [PATCH] 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 57bfcf8207..2f4a2b1461 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1683,6 +1683,17 @@ (define-public tophat '(#: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 @@ (define-public tophat (("#include ") "#include ")) #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)