From f643ef8969455a17e382ec4bc8e48e27e5a95957 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 22 Aug 2017 05:21:51 -0500
Subject: Updated gemma to latest

---
 gn/packages/gemma.scm       | 17 +++++++++--------
 gn/packages/genenetwork.scm |  6 +++---
 2 files changed, 12 insertions(+), 11 deletions(-)

(limited to 'gn')

diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 69607b3..a1481cb 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -61,30 +61,30 @@
   #:use-module (gn packages shell)
   #:use-module (srfi srfi-1))
 
-(define-public gemma-git ; guix candidate
-  (let ((commit "c91dfaef84d08ce151eecca50bf8ffdaf4b327f6"))
+(define-public gemma-git-gn2 ; guix candidate
+  (let ((commit "48da44bf2da05f76008b083923ddf5701b9c029a"))
   (package
-    (name "gemma-git")
-    (version (string-append "0.97-pre-" (string-take commit 7)))
+    (name "gemma-git-gn2")
+    (version (string-append "0.97-gn2-" (string-take commit 7)))
     (source (origin
              (method git-fetch)
              (uri (git-reference
                    (url "https://github.com/genenetwork/GEMMA")
                    (commit commit)))
-             (file-name (string-append name "-" commit))
+             (file-name (string-append name "-" version))
              (sha256
               (base32
-               "1ix4p6av88i6jfv84v2qqcmdlnxznp64bm93avrrl68v04jq6psm"))))
+               "1bvf03aimk1nywv4z8dr75f2qi8mav346w787wzddckakn29yymb"))))
     (inputs `(
               ("gsl" ,gsl)
               ("eigen" ,eigen)
+              ("shunit2" ,shunit2)
               ("lapack" ,lapack)
               ("openblas" ,openblas)
               ("zlib" ,zlib)
               ))
     (native-inputs ; for running tests
      `(("perl" ,perl)
-       ("shunit2" ,shunit2)
        ("which" ,which)
        ))
 
@@ -96,6 +96,7 @@
                        (assoc-ref %build-inputs "eigen")
                        "/include/eigen3/")
         "FORCE_DYNAMIC=1"
+        "DEBUG=1"
         "WITH_OPENBLAS=1")
        #:phases
         ; "/include/eigen3/"
@@ -118,7 +119,7 @@ mixed model and some of its close relatives for genome-wide
 association studies (GWAS).")
     (license license:gpl3))))
 
-(define-public gemma
+(define-public gemma-gn2
   (package
    (name "gemma")
    (version "0.96")
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index b55c37f..ea7fcd6 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -44,7 +44,7 @@
   #:use-module (gnu packages bootstrap)
   #:use-module (gnu packages version-control)
   #:use-module (gn packages bioinformatics)
-  ; #:use-module (gn packages gemma)
+  #:use-module (gn packages gemma)
   #:use-module (gn packages javascript)
   #:use-module (gn packages phewas)
   #:use-module (gn packages python)
@@ -175,7 +175,7 @@ location of a putative QTL.")
               ("r-wgcna" ,r-wgcna)
               ("redis" ,redis)
               ("mysql" ,mysql)
-              ("gemma" ,gemma)
+              ("gemma-git-gn2" ,gemma-git-gn2)
               ("genenetwork2-files-small" ,genenetwork2-files-small)
               ("plink-ng" ,plink-ng)
               ("pylmm-gn2" ,pylmm-gn2)
@@ -233,7 +233,7 @@ location of a putative QTL.")
                              (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" ))
                              (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
                              (plink2cmd (string-append (assoc-ref inputs "plink-ng") "/bin/plink2"))
-                             (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
+                             (gemmacmd (string-append (assoc-ref inputs "gemma-git-gn2") "/bin/gemma"))
                              )
 
                (substitute* '("etc/default_settings.py")
-- 
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