From 3093b0f1d8542ead7f992f0d0bf25a2a62ab2110 Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Thu, 16 Mar 2017 15:47:09 +0000
Subject: Moving gemma into its own module

---
 gn/packages/gemma.scm | 105 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 105 insertions(+)
 create mode 100644 gn/packages/gemma.scm

(limited to 'gn/packages/gemma.scm')

diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
new file mode 100644
index 0000000..b5ea250
--- /dev/null
+++ b/gn/packages/gemma.scm
@@ -0,0 +1,105 @@
+(define-module (gn packages gemma)
+  #: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 ant)
+  #: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 statistics)
+  #:use-module (gnu packages autotools)
+  #:use-module (gnu packages algebra)
+  #:use-module (gnu packages base)
+  #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages boost)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages databases)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages cmake)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages cpio)
+  #:use-module (gnu packages curl)
+  #:use-module (gnu packages doxygen)
+  #:use-module (gnu packages datastructures)
+  #:use-module (gnu packages check)
+  #:use-module (gnu packages file)
+  #:use-module (gnu packages gawk)
+  #:use-module (gnu packages gcc)
+  #:use-module (gnu packages graphviz)
+  #: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 mpi)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages node)
+  #:use-module (gnu packages parallel)
+  #:use-module (gnu packages pcre)
+  #: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 time)
+  #:use-module (gnu packages tls)
+  #:use-module (gnu packages vim)
+  #:use-module (gnu packages web)
+  #:use-module (gnu packages xml)
+  #:use-module (gnu packages zip)
+  #:use-module (gnu packages bootstrap)
+  #:use-module (gn packages ldc)
+  #:use-module (gn packages ldc)
+  #:use-module (gn packages shell)
+  #:use-module (srfi srfi-1))
+
+(define-public gemma-git ; guix candidate
+  (let ((commit "2de4bfab3"))
+  (package
+    (name "gemma-git")
+    (version (string-append "0.9.5-" commit ))
+    (source (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/genenetwork/GEMMA.git")
+                   (commit commit)))
+             (file-name (string-append name "-" commit))
+             (sha256
+              (base32
+               "1drffdgwbzgiw9sf55ghl3zjv58f8i9kfz0zys5mp6n06syp4ira"))))
+    (inputs `(
+              ("gsl" ,gsl)
+              ("lapack" ,lapack)
+              ("zlib" ,zlib)
+              ))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:make-flags '(" FORCE_DYNAMIC=1")
+       #:phases
+        (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'build 'bin-mkdir
+                     (lambda _
+                       (mkdir-p "bin")
+                       ))
+         (replace 'install
+                  (lambda* (#:key outputs #:allow-other-keys)
+                           (let ((out (assoc-ref outputs "out")))
+                             (install-file "bin/gemma" (string-append out "/bin"))))))
+       #:tests? #f))
+    (home-page "")
+    (synopsis "Tool for genome-wide efficient mixed model association")
+    (description "GEMMA is the software implementing the Genome-wide
+Efficient Mixed Model Association algorithm for a standard linear
+mixed model and some of its close relatives for genome-wide
+association studies (GWAS).")
+    (license license:gpl3))))
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