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Added gemma package

gn-stable
pjotrp 4 years ago
parent
commit
710fc435fa
1 changed files with 43 additions and 0 deletions
  1. +43
    -0
      gn/packages/bioinformatics.scm

+ 43
- 0
gn/packages/bioinformatics.scm View File

@@ -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)


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