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| author | Ben Woodcroft <donttrustben@gmail.com> | 2015-07-18 17:39:05 +1000 |
|---|---|---|
| committer | Mark H Weaver <mhw@netris.org> | 2015-07-19 15:17:08 -0400 |
| commit | 8fd790eb87a5adaebca9a588c597c51c84fc6cc7 (patch) | |
| tree | 90d0340a66f95897fa1b83a91ff47072d3e38e81 | |
| parent | 3ab98da1bd91a6d211475a18ba628180071b1a35 (diff) | |
| download | patches-8fd790eb87a5adaebca9a588c597c51c84fc6cc7.tar patches-8fd790eb87a5adaebca9a588c597c51c84fc6cc7.tar.gz | |
gnu: Add metabat.
* gnu/packages/bioinformatics.scm (metabat): New variable.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 79 |
1 files changed, 79 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a28832dfa8..e7eed3a694 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1394,6 +1394,85 @@ resolution of binding sites through combining the information of both sequencing tag position and orientation.") (license license:bsd-3))) + +(define-public metabat + (package + (name "metabat") + (version "0.26.1") + (source (origin + (method url-fetch) + (uri (string-append + "https://bitbucket.org/berkeleylab/metabat/get/" + version ".tar.bz2")) + (file-name (string-append name "-" version ".tar.bz2")) + (sha256 + (base32 + "0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa")))) + (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)) + (add-after 'unpack 'fix-scons + (lambda _ + (substitute* "SConstruct" ; Do not distribute README + (("^env\\.Install\\(idir_prefix, 'README\\.md'\\)") + "")) + #t)) + (delete 'configure) + (replace 'build + (lambda* (#:key inputs outputs #:allow-other-keys) + (mkdir (assoc-ref outputs "out")) + (zero? (system* "scons" + (string-append + "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 + (delete 'check) + (delete 'install)))) + (inputs + `(("zlib" ,zlib) + ("perl" ,perl) + ("samtools" ,samtools) + ("htslib" ,htslib) + ("boost" ,boost))) + (native-inputs + `(("scons" ,scons))) + (home-page "https://bitbucket.org/berkeleylab/metabat") + (synopsis + "Reconstruction of single genomes from complex microbial communities") + (description + "Grouping large genomic fragments assembled from shotgun metagenomic +sequences to deconvolute complex microbial communities, or metagenome binning, +enables the study of individual organisms and their interactions. MetaBAT is +an automated metagenome binning software, which integrates empirical +probabilistic distances of genome abundance and tetranucleotide frequency.") + (license (license:non-copyleft "file://license.txt" + "See licence.txt in the distribution.")))) + (define-public miso (package (name "miso") |