diff options
Diffstat (limited to 'gn/packages/phewas.scm')
| -rw-r--r-- | gn/packages/phewas.scm | 113 |
1 files changed, 0 insertions, 113 deletions
diff --git a/gn/packages/phewas.scm b/gn/packages/phewas.scm index e6e749c..3bfeeaa 100644 --- a/gn/packages/phewas.scm +++ b/gn/packages/phewas.scm @@ -42,37 +42,6 @@ #:use-module (gnu packages xml) #:use-module (srfi srfi-1)) -(define-public r-intermediate - (let ((commit "1e4ec77a92889f7548da766cb28abab18df952dc")) - (package - (name "r-intermediate") - (version "0.2-4") - (source (origin - ;; We use the git reference, because there's no CRAN package (yet) - (method git-fetch) - (uri (git-reference - (url "https://github.com/simecek/intermediate.git") - (commit commit))) - (file-name (string-append name "-" (string-take commit 7) "-checkout" )) - (sha256 - (base32 - "0l7acxmizw8az37365z4gr9wc6ny9d4zx3q42dgvp04yyzwafbr8")))) - (build-system r-build-system) - ; (propagated-inputs - ; `(("r-emma" ,r-emma))) - (inputs - `(("r-ggplot2" ,r-ggplot2) - ("r-magrittr" ,r-magrittr) - ("r-plotly" ,r-plotly) - ("r-htmlwidgets" ,r-htmlwidgets) - ("r-testthat" ,r-testthat))) - (synopsis "R/intermediate") - (description - "R package for eQTl/pQTL mediation analysis.") - (home-page "https://github.com/simecek/intermediate") - (license license:gpl3)))) - - (define-public r-mlmm (let ((commit "9fec9805573e97b44ee121f3651ddb79eafc8f8d")) (package @@ -98,52 +67,6 @@ genome-wide association studies in structured populations.") (home-page "https://github.com/Gregor-Mendel-Institute/mlmm") (license license:gpl3)))) -(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 "1.4.1") - (source - (origin - (method url-fetch) - (uri (bioconductor-uri "fgsea" version)) - (sha256 - (base32 - "187c8xckx0s1p19i85nsiapgb3mppjqxp7zyld5hqyjvw3zcdj50")))) - (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-qvalue-old (package (name "r-qvalue-old") @@ -165,39 +88,3 @@ genome-wide association studies in structured populations.") ".") (license license:expat))) -(define-public r-phewas ; GN2 - (package - (name "r-phewas") - (version "0.0.0-1") - (source #f) - (build-system trivial-build-system) - (propagated-inputs - `( - ("r" ,r) - ("r-data-table" ,r-data-table) - ; ("r-emma" ,r-emma) - ("r-fgsea" ,r-fgsea) - ("r-intermediate" ,r-intermediate) - ("r-limma" ,r-limma) - ("r-mlmm" ,r-mlmm) - ("r-qvalue" ,r-qvalue) - )) - (arguments - `(; #:guile ,%bootstrap-guile - #:modules ((guix build utils)) - #:builder - (let* ((out (assoc-ref %outputs "out")) - (bash (assoc-ref %build-inputs "bash")) - (foo (string-append out "/foo"))) - (begin - (use-modules (guix build utils)) - (mkdir out) - #t)))) - - (home-page - "None") - (synopsis - "None") - (description - "None.") - (license license:gpl2+))) |