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Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 51 |
1 files changed, 51 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index d81a19a..a0a375b 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -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") |