aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
authorRicardo Wurmus <rekado@elephly.net>2019-03-25 14:34:41 +0100
committerRicardo Wurmus <rekado@elephly.net>2019-03-25 14:34:41 +0100
commit80eb01c7763e99603dac6c1e4ad41f521fed5c26 (patch)
tree5003d46b17cdaf1f83496952560e7cec7ef9e28c
parentbac0ca322ce5b1140e8bdd7fb2364e8c09dc09aa (diff)
downloadguix-80eb01c7763e99603dac6c1e4ad41f521fed5c26.tar
guix-80eb01c7763e99603dac6c1e4ad41f521fed5c26.tar.gz
gnu: r-gkmsvm: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-gkmsvm): Move from here... * gnu/packages/bioconductor.scm (r-gkmsvm): ...to here.
-rw-r--r--gnu/packages/bioconductor.scm34
-rw-r--r--gnu/packages/bioinformatics.scm33
2 files changed, 34 insertions, 33 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 710b9fd07a..f687a03030 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2521,3 +2521,37 @@ summaries of the read-types produced, it provides a number of plots for
visualising metrics relative to experiment run time or spatially over the
surface of a flowcell.")
(license license:expat)))
+
+;; This is a CRAN package, but it depends on packages from Bioconductor.
+(define-public r-gkmsvm
+ (package
+ (name "r-gkmsvm")
+ (version "0.79.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "gkmSVM" version))
+ (sha256
+ (base32
+ "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
+ (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 "https://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+)))
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1a942b6476..42c90ea949 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8533,39 +8533,6 @@ 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 "0.79.0")
- (source
- (origin
- (method url-fetch)
- (uri (cran-uri "gkmSVM" version))
- (sha256
- (base32
- "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
- (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 "https://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 r-tximport
(package
(name "r-tximport")