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authorpjotrp2017-03-16 15:47:35 +0000
committerpjotrp2017-03-16 15:47:35 +0000
commitcffa2c9968e21ba1870614c1748b6d7858138534 (patch)
tree86a45c8a8c7f50f4753c07ecdf7a4929b732b7d3
parent0062de95882c896c0379f90fcfb11e2d249fccad (diff)
parent3093b0f1d8542ead7f992f0d0bf25a2a62ab2110 (diff)
downloadguix-bioinformatics-cffa2c9968e21ba1870614c1748b6d7858138534.tar.gz
Merge branch 'master' into gn-phewasgn-phewas
-rw-r--r--gn/packages/bioinformatics.scm41
-rw-r--r--gn/packages/gemma.scm105
-rw-r--r--gn/packages/genenetwork.scm1
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)