Thanks for fixing the samtools headers Ricardo, needed that for this.
>From 3f253f059edee5ee2fdb116e310ab210646acf40 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrust...@gmail.com>
Date: Sat, 11 Jul 2015 16:49:30 +1000
Subject: [PATCH] gnu: Add metabat.
* gnu/packages/bioinformatics.scm (metabat): New variable.
---
gnu/packages/bioinformatics.scm | 72 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 72 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a28832d..a349d39 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1394,6 +1394,78 @@ 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.gz"))
+ (sha256
+ (base32
+ "0vgrhbaxg4dkxyax2kbigak7w0arhqvw0szwp6gd9wmyilc44kfa"))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:tests? #f ; tests run as part of build phase
+ #:phases
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* _
+ (substitute* "SConstruct" ; Do not distribute README
+ (("env.Install.idir_prefix, 'README.md'.") ""))
+ #t))
+ (replace 'build
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (substitute* "SConstruct"
+ (("/include/bam/bam.h")
+ "/include/samtools/bam.h"))
+ (substitute* "src/BamUtils.h"
+ (("#include .bam/bam.h.")
+ "#include \"samtools/bam.h\""))
+ (substitute* "src/BamUtils.h"
+ (("#include .bam/sam.h.")
+ "#include \"samtools/sam.h\""))
+ (substitute* "src/KseqReader.h"
+ (("#include \"bam/kseq.h\"")
+ "#include \"samtools/kseq.h\""))
+ (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"))))
+ (delete 'install))))
+ (inputs
+ `(("zlib" ,zlib)
+ ("perl" ,perl)
+ ("samtools" ,samtools)
+ ("htslib" ,htslib)))
+ (native-inputs
+ `(("boost" ,boost)
+ ("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 LICENSE in the distribution."))))
+
(define-public miso
(package
(name "miso")
--
2.4.3
