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gnu: Add SEEK. 

* gnu/packages/bioinformatics.scm (seek): New variable.
master
Ricardo Wurmus 2016-06-15 15:31:40 +02:00 committed by Ricardo Wurmus
parent d6e374a0d9
commit ec9466388e
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1 changed files with 72 additions and 0 deletions
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@ -27,6 +27,7 @@
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix hg-download)
#:use-module (guix build-system ant)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
@ -51,6 +52,7 @@
#:use-module (gnu packages gcc)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages logging)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages mpi)
@ -61,6 +63,7 @@
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages readline)
#:use-module (gnu packages ruby)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
@ -3000,6 +3003,75 @@ while RNA-seq specific modules evaluate sequencing saturation, mapped reads
distribution, coverage uniformity, strand specificity, etc.")
(license license:gpl3+)))
(define-public seek
;; There are no release tarballs. According to the installation
;; instructions at http://seek.princeton.edu/installation.jsp, the latest
;; stable release is identified by this changeset ID.
(let ((changeset "2329130")
(revision "1"))
(package
(name "seek")
(version (string-append "0-" revision "." changeset))
(source (origin
(method hg-fetch)
(uri (hg-reference
(url "https://bitbucket.org/libsleipnir/sleipnir")
(changeset changeset)))
(sha256
(base32
"0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
(build-system gnu-build-system)
(arguments
`(#:modules ((srfi srfi-1)
(guix build gnu-build-system)
(guix build utils))
#:phases
(let ((dirs '("SeekMiner"
"SeekEvaluator"
"SeekPrep"
"Distancer"
"Data2DB"
"PCL2Bin")))
(modify-phases %standard-phases
(add-before 'configure 'bootstrap
(lambda _
(zero? (system* "bash" "gen_auto"))))
(add-after 'build 'build-additional-tools
(lambda* (#:key make-flags #:allow-other-keys)
(every (lambda (dir)
(with-directory-excursion (string-append "tools/" dir)
(zero? (apply system* "make" make-flags))))
dirs)))
(add-after 'install 'install-additional-tools
(lambda* (#:key make-flags #:allow-other-keys)
(fold (lambda (dir result)
(with-directory-excursion (string-append "tools/" dir)
(and result
(zero? (apply system*
`("make" ,@make-flags "install"))))))
#t dirs)))))))
(inputs
`(("gsl" ,gsl)
("boost" ,boost)
("libsvm" ,libsvm)
("readline" ,readline)
("gengetopt" ,gengetopt)
("log4cpp" ,log4cpp)))
(native-inputs
`(("autoconf" ,autoconf)
("automake" ,automake)
("perl" ,perl)))
(home-page "http://seek.princeton.edu")
(synopsis "Gene co-expression search engine")
(description
"SEEK is a computational gene co-expression search engine. SEEK provides
biologists with a way to navigate the massive human expression compendium that
now contains thousands of expression datasets. SEEK returns a robust ranking
of co-expressed genes in the biological area of interest defined by the user's
query genes. It also prioritizes thousands of expression datasets according
to the user's query of interest.")
(license license:cc-by3.0))))
(define-public samtools
(package
(name "samtools")