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authorpjotrp2017-05-17 09:39:13 +0000
committerpjotrp2017-05-17 09:39:13 +0000
commita0f4e5a7279625ecd8391f5412e54158bee51dd1 (patch)
tree710a8d36196e0acee451426ea885d08cb218f771 /gn/packages
parent0e79fde97071b8ab0d189a158a6092edd09670ff (diff)
downloadguix-bioinformatics-a0f4e5a7279625ecd8391f5412e54158bee51dd1.tar.gz
Adding stable gemma package
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/gemma.scm39
1 files changed, 38 insertions, 1 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 35ed294..6cd8388 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -95,7 +95,7 @@
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "bin/gemma" (string-append out "/bin"))))))
- #:tests? #f))
+ #:tests? #t))
(home-page "")
(synopsis "Tool for genome-wide efficient mixed model association")
(description "GEMMA is the software implementing the Genome-wide
@@ -103,3 +103,40 @@ 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 gemma
+ (package
+ (name "gemma")
+ (version "0.95a") ; this build fails
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
+ version ".tar.gz"))
+ (sha256
+ (base32
+ "1h0fqs45gy0n1nr76pzzagrv1cbcp7zaz34ljqb09jljc7c3lw9p"))))
+ (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)) ; no tests included
+ (home-page "")
+ (synopsis "Tool for genome-wide efficient mixed model association")
+ (description "GEMMA is 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)))