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authorBen Woodcroft <donttrustben@gmail.com>2015-09-30 18:35:32 +1000
committerLudovic Courtès <ludo@gnu.org>2015-10-01 10:51:28 +0200
commita2950fa4dcddb2279f974bc7d1e2ce9fa0ffa315 (patch)
treea596099c492df0b1a0f14d23d92be950226c7609
parentaae2b445a4c13649d2711e9ee1f17fae72bdea19 (diff)
gnu: Add vsearch.
* gnu/packages/bioinformatics.scm (vsearch): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
-rw-r--r--gnu/packages/bioinformatics.scm59
1 files changed, 59 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2d81f90a01..350a0d9086 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -33,6 +33,7 @@
#:use-module (guix build-system ruby)
#:use-module (guix build-system trivial)
#:use-module (gnu packages)
+ #:use-module (gnu packages autotools)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages boost)
@@ -53,6 +54,7 @@
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
+ #:use-module (gnu packages tls)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#:use-module (gnu packages xml)
@@ -2709,6 +2711,63 @@ data in the form of VCF files.")
;; at http://vcftools.sourceforge.net/license.html
(license license:lgpl3)))
+(define-public vsearch
+ (package
+ (name "vsearch")
+ (version "1.4.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (string-append
+ "https://github.com/torognes/vsearch/archive/v"
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0b1359wbzgb2cm04h7dq05v80vik88hnsv298xxd1q1f2q4ydni7"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Remove bundled cityhash and '-mtune=native'.
+ (substitute* "src/Makefile.am"
+ (("^AM_CXXFLAGS=-I\\$\\{srcdir\\}/cityhash \
+-O3 -mtune=native -Wall -Wsign-compare")
+ (string-append "AM_CXXFLAGS=-lcityhash"
+ " -O3 -Wall -Wsign-compare"))
+ (("^__top_builddir__bin_vsearch_SOURCES = cityhash/city.h \\\\")
+ "__top_builddir__bin_vsearch_SOURCES = \\")
+ (("^cityhash/config.h \\\\") "\\")
+ (("^cityhash/city.cc \\\\") "\\"))
+ (substitute* "src/vsearch.h"
+ (("^\\#include \"cityhash/city.h\"")
+ "#include <city.h>"))
+ (delete-file-recursively "src/cityhash")
+ #t))))
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (add-before 'configure 'autogen
+ (lambda _ (zero? (system* "autoreconf" "-vif")))))))
+ (inputs
+ `(("zlib" ,zlib)
+ ("bzip2" ,bzip2)
+ ("cityhash" ,cityhash)))
+ (native-inputs
+ `(("autoconf" ,autoconf)
+ ("automake" ,automake)))
+ (synopsis "Sequence search tools for metagenomics")
+ (description
+ "VSEARCH supports DNA sequence searching, clustering, chimera detection,
+dereplication, pairwise alignment, shuffling, subsampling, sorting and
+masking. The tool takes advantage of parallelism in the form of SIMD
+vectorization as well as multiple threads to perform accurate alignments at
+high speed. VSEARCH uses an optimal global aligner (full dynamic programming
+Needleman-Wunsch).")
+ (home-page "https://github.com/torognes/vsearch")
+ ;; Dual licensed; also includes public domain source.
+ (license (list license:gpl3 license:bsd-2))))
+
(define-public bio-locus
(package
(name "bio-locus")