From 710fc435fadb52bb49c65e8b1337d100c5c32c0a Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sun, 14 Feb 2016 11:16:16 +0000
Subject: Added gemma package

---
 gn/packages/bioinformatics.scm | 43 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index 096cb19..3fbab19 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -157,6 +157,48 @@ precision. It also performs bootstrap resampling to estimate the
 confidence region for the location of a putative QTL.")
     (license license:gpl2)))
 
+(define-public gemma
+  (let ((commit "2de4bfab3"))
+  (package
+    (name "gemma")
+    (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))))
+
 
 (define-public genenetwork1
   (let ((commit "d622c803b"))
@@ -231,6 +273,7 @@ confidence region for the location of a putative QTL.")
     ))
     (inputs `(
               ("mysql" ,mysql)
+              ("gemma" ,gemma)
               ("nginx" ,nginx)
               ("python2-flask" ,python2-flask)
               ("python2-htmlgen-gn" ,python2-htmlgen-gn)
-- 
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