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-rw-r--r--gn/packages/gemma.scm28
1 files changed, 21 insertions, 7 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 3c40317..9986bf5 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -63,28 +63,42 @@
#:use-module (srfi srfi-1))
(define-public gemma-git ; guix candidate
- (let ((commit "5675bdf0422f63f81752bb1fcf7b436bc30bf9b7"))
+ (let ((commit "c978835c3630286414df6076d38aad16277cdb6b"))
(package
(name "gemma-git")
- (version (string-append "0.95.2a" commit ))
+ (version (string-append "0.97-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/xiangzhou/GEMMA")
+ (url "https://github.com/genenetwork/GEMMA")
(commit commit)))
(file-name (string-append name "-" commit))
(sha256
(base32
- "0qc8dx8m4cqggnin2vsbc9l91ay6h04l0mpjv8z0wcickqb4lby6"))))
+ "1hw8y7vka79v84lv5vyhkinx864yjh1wd8vfd16cvqs1bi8qw3n2"))))
(inputs `(
("gsl" ,gsl)
+ ("eigen" ,eigen)
("lapack" ,lapack)
+ ("openblas" ,openblas)
("zlib" ,zlib)
))
+ (native-inputs ; for running tests
+ `(("shunit2" ,shunit2)
+ ("which" ,which)
+ ))
+
(build-system gnu-build-system)
(arguments
- `(#:make-flags '(" FORCE_DYNAMIC=1")
+ `(#:make-flags
+ (list
+ (string-append "EIGEN_INCLUDE_PATH="
+ (assoc-ref %build-inputs "eigen")
+ "/include/eigen3/")
+ "FORCE_DYNAMIC=1"
+ "WITH_OPENBLAS=1")
#:phases
+ ; "/include/eigen3/"
(modify-phases %standard-phases
(delete 'configure)
(add-before 'build 'bin-mkdir
@@ -95,8 +109,8 @@
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(install-file "bin/gemma" (string-append out "/bin"))))))
- #:tests? #f))
- (home-page "")
+ #:parallel-tests? #f))
+ (home-page "http://www.xzlab.org/software.html")
(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