diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 39 |
1 files changed, 12 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6d36bb73ba..95dc6aff45 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1110,9 +1110,6 @@ relying on a complex dependency tree.") (build-system cmake-build-system) (arguments `(#:parallel-build? #f)) - (inputs - `(("gcc" ,gcc-5))) ; Compilation of bpp-phyl fails with GCC 4.9 so we - ; compile all of the bpp packages with GCC 5. (home-page "http://biopp.univ-montp2.fr") (synopsis "C++ libraries for Bioinformatics") (description @@ -1148,10 +1145,7 @@ providing them a set of re-usable tools.") #:out-of-source? #f)) (inputs `(("bpp-core" ,bpp-core) - ("bpp-seq" ,bpp-seq) - ;; GCC 4.8 fails due to an 'internal compiler error', so we use a more - ;; modern GCC. - ("gcc" ,gcc-5))) + ("bpp-seq" ,bpp-seq))) (home-page "http://biopp.univ-montp2.fr") (synopsis "Bio++ phylogenetic Library") (description @@ -1183,8 +1177,7 @@ library provides phylogenetics-related modules.") #:tests? #f)) ; There are no tests. (inputs `(("bpp-core" ,bpp-core) - ("bpp-seq" ,bpp-seq) - ("gcc" ,gcc-5))) + ("bpp-seq" ,bpp-seq))) (home-page "http://biopp.univ-montp2.fr") (synopsis "Bio++ population genetics library") (description @@ -1217,8 +1210,7 @@ library provides population genetics-related modules.") ;; so the tests fail. #:out-of-source? #f)) (inputs - `(("bpp-core" ,bpp-core) - ("gcc" ,gcc-5))) ; Use GCC 5 as per 'bpp-core'. + `(("bpp-core" ,bpp-core))) (home-page "http://biopp.univ-montp2.fr") (synopsis "Bio++ sequence library") (description @@ -1256,8 +1248,7 @@ library provides sequence-related modules.") `(("bpp-core" ,bpp-core) ("bpp-seq" ,bpp-seq) ("bpp-phyl" ,bpp-phyl) - ("bpp-phyl" ,bpp-popgen) - ("gcc" ,gcc-5))) + ("bpp-phyl" ,bpp-popgen))) (home-page "http://biopp.univ-montp2.fr") (synopsis "Bioinformatics tools written with the Bio++ libraries") (description @@ -3261,9 +3252,7 @@ comment or quality sections.") (lambda* (#:key inputs #:allow-other-keys) ;; Ensure that Eigen headers can be found (setenv "CPLUS_INCLUDE_PATH" - (string-append (getenv "CPLUS_INCLUDE_PATH") - ":" - (assoc-ref inputs "eigen") + (string-append (assoc-ref inputs "eigen") "/include/eigen3")) #t)) (add-before 'build 'bin-mkdir @@ -4848,7 +4837,7 @@ generated using the PacBio Iso-Seq protocol.") (define-public prank (package (name "prank") - (version "150803") + (version "170427") (source (origin (method url-fetch) (uri (string-append @@ -4856,7 +4845,7 @@ generated using the PacBio Iso-Seq protocol.") version ".tgz")) (sha256 (base32 - "0am4z94fs3w2n5xpfls9zda61vq7qqz4q2i7b9hlsxz5q4j3kfm4")))) + "0nc8g9c5rkdxcir46s0in9ci1sxwzbjibxrvkksf22ybnplvagk2")))) (build-system gnu-build-system) (arguments `(#:phases @@ -11713,9 +11702,7 @@ bytes of memory space, where n is the length of the string.") ;; Ensure that Eigen headers can be found (setenv "CPLUS_INCLUDE_PATH" - (string-append (getenv "CPLUS_INCLUDE_PATH") - ":" - (assoc-ref inputs "eigen") + (string-append (assoc-ref inputs "eigen") "/include/eigen3")) #t))))) (inputs @@ -11894,14 +11881,11 @@ The following file formats are supported: (("lib/libdivsufsort.a") "/lib/libdivsufsort.so")) ;; Ensure that all headers can be found - (setenv "CPLUS_INCLUDE_PATH" - (string-append (getenv "CPLUS_INCLUDE_PATH") + (setenv "CPATH" + (string-append (getenv "CPATH") ":" (assoc-ref inputs "eigen") "/include/eigen3")) - (setenv "CPATH" - (string-append (assoc-ref inputs "eigen") - "/include/eigen3")) #t)) ;; CMAKE_INSTALL_PREFIX does not exist when the tests are ;; run. It only exists after the install phase. @@ -14094,7 +14078,8 @@ choosing which reads pass the filter.") (lambda* (#:key inputs #:allow-other-keys) (setenv "CPATH" (string-append (assoc-ref inputs "eigen") - "/include/eigen3")) + "/include/eigen3:" + (or (getenv "CPATH") ""))) #t)) (delete 'configure) (replace 'install |