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authorpjotrp2017-02-27 09:07:10 +0000
committerpjotrp2017-02-27 09:07:10 +0000
commit335efa9bebd01e75b36fb5505f4843f0cc795a36 (patch)
tree5e6c013736d15a6a6e668d2bdd9d3586ecaf6cc4 /gn/packages
parentee9c6e5fed733634c749659c3ccbd05a5909e217 (diff)
downloadguix-bioinformatics-335efa9bebd01e75b36fb5505f4843f0cc795a36.tar.gz
r-fgsea: added with dependency r-fastmatch
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/phewas.scm52
1 files changed, 50 insertions, 2 deletions
diff --git a/gn/packages/phewas.scm b/gn/packages/phewas.scm
index d3a1288..c5e8812 100644
--- a/gn/packages/phewas.scm
+++ b/gn/packages/phewas.scm
@@ -41,9 +41,55 @@
#:use-module (gnu packages bootstrap)
#:use-module (srfi srfi-1))
-(define-public r-auwerxlab ; GN2
+(define-public r-fastmatch
+(package
+ (name "r-fastmatch")
+ (version "1.1-0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (cran-uri "fastmatch" version))
+ (sha256
+ (base32
+ "0z80jxkygmzn11sq0c2iz357s9bpki548lg926g85gldhfj1md90"))))
+ (build-system r-build-system)
+ (home-page "http://www.rforge.net/fastmatch")
+ (synopsis "Fast match() function")
+ (description
+ "Package providing a fast match() replacement for cases that require repeated look-ups. It is slightly faster that R's built-in match() function on first match against a table, but extremely fast on any subsequent lookup as it keeps the hash table in memory.")
+ (license license:gpl2)))
+
+(define-public r-fgsea
+ (package
+ (name "r-fgsea")
+ (version "1.0.2")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "fgsea" version))
+ (sha256
+ (base32
+ "1yq4s4g4xxzcpkv9dpbg29444iy38vfgwj4wgr47rjjq8njfblfx"))))
+ (build-system r-build-system)
+ ; (native-inputs
+ ; `(("gfortran" ,gfortran)))
+ ; ‘Rcpp’, ‘data.table’, ‘BiocParallel’, ‘ggplot2’, ‘gridExtra’, ‘fastmatch
+ (propagated-inputs
+ `(("r-rcpp" ,r-rcpp)
+ ("r-data-table" ,r-data-table)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-fastmatch" ,r-fastmatch)))
+ (home-page "http://bioconductor.org/packages/fgsea")
+ (synopsis "")
+ (description
+ ".")
+ (license license:expat)))
+
+(define-public r-phewas ; GN2
(package
- (name "r-auwerxlab")
+ (name "r-phewas")
(version "0.0.0-1")
(source #f)
(build-system trivial-build-system)
@@ -51,6 +97,8 @@
`(
("r" ,r)
("r-data-table" ,r-data-table)
+ ("r-fgsea" ,r-fgsea)
+ ("r-limma" ,r-limma)
))
(arguments
`(#:guile ,%bootstrap-guile