From 335efa9bebd01e75b36fb5505f4843f0cc795a36 Mon Sep 17 00:00:00 2001 From: pjotrp Date: Mon, 27 Feb 2017 09:07:10 +0000 Subject: r-fgsea: added with dependency r-fastmatch --- gn/packages/phewas.scm | 52 ++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file 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 -- cgit v1.2.3