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[18/18] gnu: Add r-gkmsvm.

Message ID 20161124165139.13740-19-rekado@elephly.net
State New
Headers show

Commit Message

Ricardo Wurmus Nov. 24, 2016, 4:51 p.m. UTC
* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
---
 gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
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Patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 89a9db1..844bb8e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7551,6 +7551,39 @@  bound and non bound genomic regions to accurately identify transcription
 factors bound at the specific regions.")
     (license license:gpl2+)))
 
+(define-public r-gkmsvm
+  (package
+    (name "r-gkmsvm")
+    (version "0.71.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "gkmSVM" version))
+       (sha256
+        (base32
+         "1zpxgxmf2nd5j5wn00ps6kfxr8wxh7d1swr1rr4spq7sj5z5z0k0"))))
+    (properties `((upstream-name . "gkmSVM")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-kernlab" ,r-kernlab)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rocr" ,r-rocr)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-seqinr" ,r-seqinr)))
+    (home-page "http://cran.r-project.org/web/packages/gkmSVM")
+    (synopsis "Gapped-kmer support vector machine")
+    (description
+     "This R package provides tools for training gapped-kmer SVM classifiers
+for DNA and protein sequences.  This package supports several sequence
+kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
+    (license license:gpl2+)))
+
 (define-public emboss
   (package
     (name "emboss")