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authorpjotrp2016-02-14 11:16:16 +0000
committerpjotrp2016-02-14 11:16:16 +0000
commit710fc435fadb52bb49c65e8b1337d100c5c32c0a (patch)
tree043544eff5e87b5fb86f457f870c960d0cd526d4 /gn
parent04419a9ff0ca2d9b258503bf1e8dd97c77e6e9a3 (diff)
downloadguix-bioinformatics-710fc435fadb52bb49c65e8b1337d100c5c32c0a.tar.gz
Added gemma package
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/bioinformatics.scm43
1 files changed, 43 insertions, 0 deletions
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)