diff options
| author | Ben Woodcroft <donttrustben@gmail.com> | 2016-06-28 21:28:06 +1000 |
|---|---|---|
| committer | Ben Woodcroft <donttrustben@gmail.com> | 2016-06-28 21:28:06 +1000 |
| commit | 45469ebe528df81e6c3a7b4aa5a42f914dc28acd (patch) | |
| tree | c4a4019404a0ade3681d452257db6e12bbc85e8f /gnu/packages/bioinformatics.scm | |
| parent | af45244e3662d324f37923c7fa120e49673b3ad2 (diff) | |
| download | patches-45469ebe528df81e6c3a7b4aa5a42f914dc28acd.tar patches-45469ebe528df81e6c3a7b4aa5a42f914dc28acd.tar.gz | |
gnu: metabat: Update to 0.26.3.
* gnu/packages/bioinformatics.scm (metabat): Update to 0.26.3.
[arguments]: Update include and linking paths accordingly.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 57 |
1 files changed, 30 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7ae3593181..fa0979bcea 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2486,7 +2486,7 @@ sequences).") (define-public metabat (package (name "metabat") - (version "0.26.1") + (version "0.26.3") (source (origin (method url-fetch) (uri (string-append @@ -2495,31 +2495,40 @@ sequences).") (file-name (string-append name "-" version ".tar.bz2")) (sha256 (base32 - "0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa")))) + "1vpfvgsn8wdsv1g7z73zxcncskx7dy7bw5msg1hhibk25ay11pyg")))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-includes - (lambda _ - (substitute* "SConstruct" - (("/include/bam/bam.h") - "/include/samtools/bam.h")) - (substitute* "src/BamUtils.h" - (("^#include \"bam/bam\\.h\"") - "#include \"samtools/bam.h\"") - (("^#include \"bam/sam\\.h\"") - "#include \"samtools/sam.h\"")) - (substitute* "src/KseqReader.h" - (("^#include \"bam/kseq\\.h\"") - "#include \"samtools/kseq.h\"")) - #t)) + (lambda _ + (substitute* "src/BamUtils.h" + (("^#include \"bam/bam\\.h\"") + "#include \"samtools/bam.h\"") + (("^#include \"bam/sam\\.h\"") + "#include \"samtools/sam.h\"")) + (substitute* "src/KseqReader.h" + (("^#include \"bam/kseq\\.h\"") + "#include \"htslib/kseq.h\"")) + #t)) (add-after 'unpack 'fix-scons - (lambda _ - (substitute* "SConstruct" ; Do not distribute README - (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") - "")) - #t)) + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "SConstruct" + (("^htslib_dir = 'samtools'") + (string-append "hitslib_dir = '" + (assoc-ref inputs "htslib") + "'")) + (("^samtools_dir = 'samtools'") + (string-append "samtools_dir = '" + (assoc-ref inputs "htslib") + "'")) + (("^findStaticOrShared\\('bam', hts_lib") + (string-append "findStaticOrShared('bam', '" + (assoc-ref inputs "samtools") + "/lib'")) + ;; Do not distribute README. + (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") "")) + #t)) (delete 'configure) (replace 'build (lambda* (#:key inputs outputs #:allow-other-keys) @@ -2529,16 +2538,10 @@ sequences).") "PREFIX=" (assoc-ref outputs "out")) (string-append - "HTSLIB_DIR=" - (assoc-ref inputs "htslib")) - (string-append - "SAMTOOLS_DIR=" - (assoc-ref inputs "samtools")) - (string-append "BOOST_ROOT=" (assoc-ref inputs "boost")) "install")))) - ;; check and install carried out during build phase + ;; Check and install are carried out during build phase. (delete 'check) (delete 'install)))) (inputs |