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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2016-06-15 15:31:40 +0200
committerRicardo Wurmus <rekado@elephly.net>2016-06-28 22:49:05 +0200
commitec9466388ed03976714d3d9706bced9a288f11a6 (patch)
treee479aa4ef6180e79f0ae318c7f4cee7b89aa6aa5 /gnu/packages/bioinformatics.scm
parentd6e374a0d9a71fac7f3946aaa56205d25d99916d (diff)
downloadgnu-guix-ec9466388ed03976714d3d9706bced9a288f11a6.tar
gnu-guix-ec9466388ed03976714d3d9706bced9a288f11a6.tar.gz
gnu: Add SEEK.
* gnu/packages/bioinformatics.scm (seek): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm72
1 files changed, 72 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 499025e29b..f944c7bbcd 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -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")