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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-12-18 17:40:02 +0100
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-01-06 11:10:46 +0100
commit43c565d2e729cf3405da51be6360dcc741691afd (patch)
tree64828793d55b05df450b167df4b567e8c8ca9ea5 /gnu/packages/bioinformatics.scm
parent03cea32031bf9d641022f199f16e2eb898ff9bd3 (diff)
gnu: Add Jellyfish.
* gnu/packages/bioinformatics.scm (jellyfish): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm50
1 files changed, 50 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 76a1c17737..f1f7968908 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -56,6 +56,7 @@
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
+ #:use-module (gnu packages time)
#:use-module (gnu packages tls)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
@@ -1738,6 +1739,55 @@ to measure the reproducibility of findings identified from replicate
experiments and provide highly stable thresholds based on reproducibility.")
(license license:gpl3+)))
+(define-public jellyfish
+ (package
+ (name "jellyfish")
+ (version "2.2.4")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/gmarcais/Jellyfish/"
+ "releases/download/v" version
+ "/jellyfish-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0a6xnynqy2ibfbfz86b9g2m2dgm7f1469pmymkpam333gi3p26nk"))))
+ (build-system gnu-build-system)
+ (outputs '("out" ;for library
+ "ruby" ;for Ruby bindings
+ "python")) ;for Python bindings
+ (arguments
+ `(#:configure-flags
+ (list (string-append "--enable-ruby-binding="
+ (assoc-ref %outputs "ruby"))
+ (string-append "--enable-python-binding="
+ (assoc-ref %outputs "python")))
+ #:phases
+ (modify-phases %standard-phases
+ (add-before 'check 'set-SHELL-variable
+ (lambda _
+ ;; generator_manager.hpp either uses /bin/sh or $SHELL
+ ;; to run tests.
+ (setenv "SHELL" (which "bash"))
+ #t)))))
+ (native-inputs
+ `(("bc" ,bc)
+ ("time" ,time)
+ ("ruby" ,ruby)
+ ("python" ,python-2)))
+ (synopsis "Tool for fast counting of k-mers in DNA")
+ (description
+ "Jellyfish is a tool for fast, memory-efficient counting of k-mers in
+DNA. A k-mer is a substring of length k, and counting the occurrences of all
+such substrings is a central step in many analyses of DNA sequence. Jellyfish
+is a command-line program that reads FASTA and multi-FASTA files containing
+DNA sequences. It outputs its k-mer counts in a binary format, which can be
+translated into a human-readable text format using the @code{jellyfish dump}
+command, or queried for specific k-mers with @code{jellyfish query}.")
+ (home-page "http://www.genome.umd.edu/jellyfish.html")
+ ;; The combined work is published under the GPLv3 or later. Individual
+ ;; files such as lib/jsoncpp.cpp are released under the Expat license.
+ (license (list license:gpl3+ license:expat))))
+
(define-public macs
(package
(name "macs")