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authorRoel Janssen2016-03-16 13:49:52 +0100
committerRoel Janssen2016-03-16 13:49:52 +0100
commite024f97ea8886191fa49d56782dc42954bdc9880 (patch)
tree7d5ead1722a886e05d5761c2140f2f7176f00f8b /gn
parenta30321a25267f80df6084104c8d562dc61046c1f (diff)
downloadguix-bioinformatics-e024f97ea8886191fa49d56782dc42954bdc9880.tar.gz
Add delly.
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm56
1 files changed, 56 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index a0a375b..a4d14b0 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -113,6 +113,62 @@ standard alignment formats (BAM/SAM) and outputs in variant call format
package.")
(license license:gpl3+)))
+(define boost-delly
+ (package (inherit boost)
+ (name "boost-delly")
+ (version "1.57.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append
+ "mirror://sourceforge/boost/boost_"
+ (string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)
+ ".tar.bz2"))
+ (sha256
+ (base32
+ "0rs94vdmg34bwwj23fllva6mhrml2i7mvmlb11zyrk1k5818q34i"))))))
+
+(define-public delly
+ (package
+ (name "delly")
+ (version "0.7.2")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/tobiasrausch/delly/archive/v"
+ version ".tar.gz"))
+ (sha256
+ (base32 "173mmg43dbxqkyq0kiffz63xbmggr2kzd55mwxci9yfh5md1zprn"))
+ (patches (list (search-patch "delly-use-system-libraries.patch")))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("python" ,python-2)))
+ (inputs
+ `(("boost" ,boost-delly) ; Use version 1.57.0 instead.
+ ("htslib" ,htslib)
+ ("zlib" ,zlib)
+ ("bzip2" ,bzip2)))
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda _
+ (let ((bin (string-append (assoc-ref %outputs "out") "/bin")))
+ (install-file "src/cov" bin)
+ (install-file "src/delly" bin)
+ (install-file "src/extract" bin)
+ (install-file "src/iover" bin)
+ (install-file "src/stats" bin)))))))
+ (home-page "https://github.com/tobiasrausch/delly")
+ (synopsis "Integrated structural variant prediction method")
+ (description "Delly is an integrated structural variant prediction method
+that can discover and genotype deletions, tandem duplications, inversions and
+translocations at single-nucleotide resolution in short-read massively parallel
+sequencing data. It uses paired-ends and split-reads to sensitively and
+accurately delineate genomic rearrangements throughout the genome. Structural
+variants can be visualized using Delly-maze and Delly-suave.")
+ (license license:gpl3)))
+
(define-public freec
(package
(name "control-freec")