diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 26 |
1 files changed, 24 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 477ad60f71..7c21586fcf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2133,7 +2133,19 @@ data and settings.") (base32 "0rah9ja4m0rl5mldd6vag9rwrivw1zrqxssfq8qx64m7961fp68k")))) (build-system cmake-build-system) - (arguments `(#:tests? #f)) ; there are no tests + (arguments + `(#:tests? #f ; there are no tests + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'add-missing-includes + (lambda _ + (substitute* "src/executioninformation.hpp" + (("#define EXECUTIONINFORMATION_HPP" line) + (string-append line "\n#include <random>"))) + (substitute* "src/plasma/fasta.hpp" + (("#define FASTA_HPP" line) + (string-append line "\n#include <random>"))) + #t))))) (inputs `(("boost" ,boost) ("cairo" ,cairo))) @@ -3138,7 +3150,10 @@ command, or queried for specific k-mers with @code{jellyfish query}.") `(("zlib" ,zlib) ("bzip2" ,bzip2) ("python-screed" ,python-screed) - ("python-bz2file" ,python-bz2file))) + ("python-bz2file" ,python-bz2file) + ;; Tests fail when gcc-5 is used for compilation. Use gcc-4.9 at least + ;; until the next version of khmer (likely 2.1) is released. + ("gcc" ,gcc-4.9))) (home-page "https://khmer.readthedocs.org/") (synopsis "K-mer counting, filtering and graph traversal library") (description "The khmer software is a set of command-line tools for @@ -5210,6 +5225,13 @@ against local background noises.") (("#include \"(bam|sam|kstring).h\"" _ header) (string-append "#include <samtools/" header ".h>"))) #t)) + (add-after 'unpack 'remove-duplicate-typedef + (lambda _ + ;; This typedef conflicts with the typedef in + ;; glibc-2.25/include/bits/types.h + (substitute* "gclib/GThreads.h" + (("typedef long long __intmax_t;") "")) + #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin/"))) |