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;; To use this file to build HEAD of gemma:
;;
;; guix build -f guix.scm
;;
;; To get a development container (e.g., run in emacs shell).
;;
;; guix environment -C -l guix.scm
(use-modules
((guix licenses) #:prefix license:)
(guix gexp)
(guix packages)
(guix git-download)
(guix build-system meson)
(gnu packages algebra)
(gnu packages base)
(gnu packages compression)
(gnu packages bioinformatics)
(gnu packages build-tools)
(gnu packages curl)
(gnu packages llvm)
(gnu packages maths)
(gnu packages ninja)
(gnu packages parallel)
(gnu packages perl)
(gnu packages perl6)
(gnu packages pkg-config)
;; (gnu packages shell) ;; for shunit2
(srfi srfi-1)
(ice-9 popen)
(ice-9 rdelim))
(define %source-dir (dirname (current-filename)))
(define %git-commit
(read-string (open-pipe "git show HEAD | head -1 | cut -d ' ' -f 2" OPEN_READ)))
(define-public gemma-git
(package
(name "gemma-git")
(version (git-version "0.98.4-pre" "HEAD" %git-commit))
(source (local-file %source-dir #:recursive? #t))
(build-system meson-build-system)
(inputs `(
("gsl" ,gsl)
;; ("shunit2" ,shunit2) ;; comes with gemma
("openblas" ,openblas)
("zlib" ,zlib)
))
(native-inputs ; for running tests
`(("perl" ,perl)
("which" ,which)
))
(home-page "https://github.com/genetics-statistics")
(synopsis "Tool for genome-wide efficient mixed model association")
(description "Genome-wide Efficient Mixed Model Association (GEMMA)
provides a standard linear mixed model resolver with application in
genome-wide association studies (GWAS).")
(license license:gpl3)))
gemma-git
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