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authorBen Woodcroft <donttrustben@gmail.com>2015-07-18 17:39:05 +1000
committerMark H Weaver <mhw@netris.org>2015-07-19 15:17:08 -0400
commit8fd790eb87a5adaebca9a588c597c51c84fc6cc7 (patch)
tree90d0340a66f95897fa1b83a91ff47072d3e38e81 /gnu
parent3ab98da1bd91a6d211475a18ba628180071b1a35 (diff)
gnu: Add metabat.
* gnu/packages/bioinformatics.scm (metabat): New variable.
Diffstat (limited to 'gnu')
-rw-r--r--gnu/packages/bioinformatics.scm79
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")