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Diffstat (limited to 'gn/packages/gemma.scm')
| -rw-r--r-- | gn/packages/gemma.scm | 105 |
1 files changed, 105 insertions, 0 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm new file mode 100644 index 0000000..b5ea250 --- /dev/null +++ b/gn/packages/gemma.scm @@ -0,0 +1,105 @@ +(define-module (gn packages gemma) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages) + #:use-module (guix utils) + #:use-module (guix download) + #:use-module (guix git-download) + #:use-module (guix build-system ant) + #:use-module (guix build-system gnu) + #:use-module (guix build-system cmake) + #:use-module (guix build-system perl) + #:use-module (guix build-system python) + ;; #:use-module (guix build-system ruby) + #:use-module (guix build-system r) + #:use-module (guix build-system trivial) + #:use-module (gn packages statistics) + #:use-module (gnu packages autotools) + #:use-module (gnu packages algebra) + #:use-module (gnu packages base) + #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages boost) + #:use-module (gnu packages compression) + #:use-module (gnu packages databases) + #:use-module (gnu packages check) + #:use-module (gnu packages cmake) + #:use-module (gnu packages compression) + #:use-module (gnu packages cpio) + #:use-module (gnu packages curl) + #:use-module (gnu packages doxygen) + #:use-module (gnu packages datastructures) + #:use-module (gnu packages check) + #:use-module (gnu packages file) + #:use-module (gnu packages gawk) + #:use-module (gnu packages gcc) + #:use-module (gnu packages graphviz) + #:use-module (gnu packages java) + #:use-module (gnu packages linux) + #:use-module (gnu packages machine-learning) + #:use-module (gnu packages maths) + #:use-module (gnu packages mpi) + #:use-module (gnu packages ncurses) + #:use-module (gnu packages node) + #:use-module (gnu packages parallel) + #:use-module (gnu packages pcre) + #:use-module (gnu packages perl) + #:use-module (gnu packages pkg-config) + #:use-module (gnu packages popt) + #:use-module (gnu packages protobuf) + #:use-module (gnu packages python) + #:use-module (gnu packages ruby) + #:use-module (gnu packages statistics) + #:use-module (gnu packages tbb) + #:use-module (gnu packages textutils) + #:use-module (gnu packages time) + #:use-module (gnu packages tls) + #:use-module (gnu packages vim) + #:use-module (gnu packages web) + #:use-module (gnu packages xml) + #:use-module (gnu packages zip) + #:use-module (gnu packages bootstrap) + #:use-module (gn packages ldc) + #:use-module (gn packages ldc) + #:use-module (gn packages shell) + #:use-module (srfi srfi-1)) + +(define-public gemma-git ; guix candidate + (let ((commit "2de4bfab3")) + (package + (name "gemma-git") + (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)))) |