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Add contra.

gn-stable
Roel Janssen 4 years ago
parent
commit
a30321a252
1 changed files with 51 additions and 0 deletions
  1. +51
    -0
      gn/packages/bioinformatics.scm

+ 51
- 0
gn/packages/bioinformatics.scm View File

@@ -62,6 +62,57 @@
#:use-module (gnu packages bootstrap)
#:use-module (srfi srfi-1))

(define-public contra
(package
(name "contra")
(version "2.0.6")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/contra-cnv/CONTRA.v" version ".tar.gz"))
(sha256
(base32
"0agpcm2xh5f0i9n9sx1kvln6mzdksddmh11bvzj6bh76yw5pnw91"))))
(build-system gnu-build-system)
(propagated-inputs
`(("python" ,python-2)
("r" ,r)
("r-dnacopy" ,r-dnacopy)
("bedtools" ,bedtools)
("samtools" ,samtools)))
(arguments
`(#:tests? #f ; There are no tests.
#:phases
(modify-phases %standard-phases
(delete 'configure)
(delete 'build) ; We can use Guix's BEDtools instead.
(replace 'install
(lambda _
(let* ((out (assoc-ref %outputs "out"))
(bin (string-append out "/bin"))
(doc (string-append out "/share/doc/contra")))
(mkdir-p bin)
(mkdir-p doc)
(and
(zero? (system* "cp" "--recursive" "scripts" bin))
(zero? (system* "cp" "contra.py" bin))
(zero? (system* "cp" "baseline.py" bin))
;; There's only a pre-built PDF available.
(zero? (system* "cp" "CONTRA_User_Guide.2.0.pdf" doc)))))))))
(home-page "http://contra-cnv.sourceforge.net/")
(synopsis "Tool for copy number variation (CNV) detection for targeted
resequencing data")
(description "CONTRA is a tool for copy number variation (CNV) detection
for targeted resequencing data such as those from whole-exome capture data.
CONTRA calls copy number gains and losses for each target region with key
strategies including the use of base-level log-ratios to remove GC-content
bias, correction for an imbalanced library size effect on log-ratios, and the
estimation of log-ratio variations via binning and interpolation. It takes
standard alignment formats (BAM/SAM) and outputs in variant call format
(VCF 4.0) for easy integration with other next generation sequencing analysis
package.")
(license license:gpl3+)))

(define-public freec
(package
(name "control-freec")


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