diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 63 |
1 files changed, 63 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2d81f90a01..0e0a886cc0 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) @@ -673,6 +675,7 @@ multiple sequence alignments.") (uri (string-append "https://github.com/YeoLab/clipper/archive/" version ".tar.gz")) + (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "1q7jpimsqln7ic44i8v2rx2haj5wvik8hc1s2syd31zcn0xk1iyq")) @@ -2709,6 +2712,66 @@ 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") + ;; vsearch uses non-portable SSE intrinsics so building fails on other + ;; platforms. + (supported-systems '("x86_64-linux")) + ;; Dual licensed; also includes public domain source. + (license (list license:gpl3 license:bsd-2)))) + (define-public bio-locus (package (name "bio-locus") |