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(define-module (gn packages phewas)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix utils)
#:use-module (guix download)
#:use-module (guix git-download)
#:use-module (guix build-system gnu)
#:use-module (guix build-system cmake)
#:use-module (guix build-system perl)
#:use-module (guix build-system python)
#:use-module (guix build-system ruby)
#:use-module (guix build-system r)
#:use-module (guix build-system trivial)
#:use-module (gn packages lmm)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
#:use-module (gnu packages bioconductor)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
#:use-module (gnu packages cran)
#:use-module (gnu packages file)
#:use-module (gnu packages gcc)
#:use-module (gnu packages java)
#:use-module (gnu packages linux)
#:use-module (gnu packages machine-learning)
#:use-module (gnu packages maths)
#:use-module (gnu packages ncurses)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages popt)
#:use-module (gnu packages protobuf)
#:use-module (gnu packages python)
#:use-module (gnu packages ruby)
#:use-module (gnu packages statistics)
#:use-module (gnu packages tbb)
#:use-module (gnu packages textutils)
#:use-module (gnu packages vim)
#:use-module (gnu packages web)
#: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
(name "r-mlmm")
(version "0.1.0")
(source (origin
;; We use the git reference, because there's no CRAN package (yet)
(method git-fetch)
(uri (git-reference
(url "https://github.com/Gregor-Mendel-Institute/mlmm.git")
(commit commit)))
(file-name (string-append name "-" (string-take commit 7) "-checkout" ))
(sha256
(base32
"0dr77bf6i7qpi6kvay84p4lgib20l552ph8mp56v3qk0fbsamh8j"))))
(build-system r-build-system)
(propagated-inputs
`(("r-emma" ,r-emma)))
(synopsis "R/mlmm")
(description
"Implements an efficient multi-locus mixed-model approach for
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")
(version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "qvalue" version))
(sha256
(base32
"1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-reshape2" ,r-reshape2)
("r-ggplot2" ,r-ggplot2)))
(home-page "http://bioconductor.org/packages/qvalue")
(synopsis "")
(description
".")
(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+)))
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