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| -rw-r--r-- | gn/packages/bioinformatics.scm | 43 |
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) |