Merge branch 'master' into gn-phewasgn-phewas

3 files changed, 106 insertions, 41 deletions

diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index efb9470..13eda3a 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -807,47 +807,6 @@ integration with gPLINK and Haploview, there is some support for the
 subsequent visualization, annotation and storage of results.")
     (license license:gpl3+))))
 
-(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))))
 
 (define-public vcflib ; duplicate? See above
   (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
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))))
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 29915b2..5702941 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -44,6 +44,7 @@
   #:use-module (gnu packages zip)
   #:use-module (gnu packages bootstrap)
   #:use-module (gn packages bioinformatics)
+  #:use-module (gn packages gemma)
   #:use-module (gn packages phewas)
   #:use-module (gn packages python)
   #:use-module (gn packages statistics)