Added guix.scm build configuration

1 files changed, 61 insertions, 0 deletions

diff --git a/guix.scm b/guix.scm
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+;; To use this file to build HEAD of gemma:
+;;
+;;   guix build -f guix.scm
+;;
+;; To get a development container (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