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(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 documentation)
#: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 "5675bdf0422f63f81752bb1fcf7b436bc30bf9b7"))
(package
(name "gemma-git")
(version (string-append "0.95.2a" commit ))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/xiangzhou/GEMMA")
(commit commit)))
(file-name (string-append name "-" commit))
(sha256
(base32
"0qc8dx8m4cqggnin2vsbc9l91ay6h04l0mpjv8z0wcickqb4lby6"))))
(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? #t))
(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 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)))
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