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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 bootstrap)
#:use-module (gn packages ldc)
#:use-module (gn packages ldc)
#:use-module (gn packages shell)
#:use-module (srfi srfi-1))
(define-public openblas-parallel
(package
(name "openblas-parallel")
(version "0.2.20")
(source
(origin
(method url-fetch)
(uri (string-append "https://github.com/xianyi/OpenBLAS/tarball/v"
version))
(file-name (string-append name "-" version ".tar.gz"))
(sha256
(base32
"1bd03c5xni0bla0wg1wba841b36b0sg13sjja955kn5xzvy4i61a"))))
(build-system gnu-build-system)
(arguments
`(
#:tests? #f ;no "check" target
;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no
;; TARGET is specified, OpenBLAS will tune itself to the build host, so
;; we need to disable substitutions.
#:substitutable?
,(let ((system (or (%current-target-system) (%current-system))))
(or (string-prefix? "x86_64" system)
(string-prefix? "i686" system)
(string-prefix? "mips" system)
(string-prefix? "aarch64" system)))
#:make-flags
(list (string-append
"PREFIX=" (assoc-ref %outputs "out"))
"SHELL=bash"
"NUM_THREADS=64"
"BINARY=64"
"NO_WARMUP=0"
"GEMM_MULTITHREAD_THRESHOLD=4"
"USE_THREAD=1"
"NO_AFFINITY=0"
"NO_LAPACK=1"
;; Build the library for all supported CPUs. This allows
;; switching CPU targets at runtime with the environment variable
;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type.
;; Unfortunately, this is not supported on non-x86 architectures,
;; where it leads to failed builds.
,@(let ((system (or (%current-target-system) (%current-system))))
(cond
((or (string-prefix? "x86_64" system)
(string-prefix? "i686" system))
'("BINARY=64 NO_WARMUP=0 GEMM_MULTITHREAD_THRESHOLD=4 USE_THREAD=1 NO_AFFINITY=0 NO_LAPACK=1 NUM_THREADS=64"))
;; On MIPS we force the "SICORTEX" TARGET, as for the other
;; two available MIPS targets special extended instructions
;; for Loongson cores are used.
((string-prefix? "mips" system)
'("TARGET=SICORTEX"))
;; On aarch64 force the generic 'armv8-a' target
((string-prefix? "aarch64" system)
'("TARGET=ARMV8"))
(else '()))))
;; no configure script
#:phases (alist-delete 'configure %standard-phases)))
(inputs
`(("gfortran" ,gfortran)
("gfortran:lib" ,gfortran "lib")))
(native-inputs
`(("cunit" ,cunit)
("perl" ,perl)))
(home-page "http://www.openblas.net/")
(synopsis "Optimized BLAS library based on GotoBLAS")
(description
"OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.")
(license license:bsd-3)))
(define-public gsl1 ; supporting older GSL tests
(package
(name "gsl1")
(version "1.16")
(source (origin
(method url-fetch)
(uri (string-append "mirror://gnu/gsl/gsl-"
version ".tar.gz"))
(sha256
(base32
"0lrgipi0z6559jqh82yx8n4xgnxkhzj46v96dl77hahdp58jzg3k"))
))
(build-system gnu-build-system)
(home-page "https://www.gnu.org/software/gsl/")
(synopsis "Numerical library for C and C++")
(description
"The GNU Scientific Library is a library for numerical analysis in C
and C++. It includes a wide range of mathematical routines, with over 1000
functions in total. Subject areas covered by the library include:
differential equations, linear algebra, Fast Fourier Transforms and random
numbers.")
(license license:gpl3+)))
(define-public gemma-git-gn2 ; guix candidate
(let ((commit "e69b71e0ea4ee307dca5f48c48a21103129c8635"))
(package
(name "gemma-git-gn2")
(version (string-append "0.97-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/genenetwork/GEMMA")
(commit commit)))
(file-name (string-append name "-" version "-checkout"))
(sha256
(base32
"0xfny3cmh4y78jhhr0dnnyywsc5kx91jvxdnbpsy2xfg2imm46mq"))))
(inputs `(
("gsl" ,gsl)
("eigen" ,eigen)
("shunit2" ,shunit2)
("lapack" ,lapack)
("openblas-parallel" ,openblas-parallel)
("zlib" ,zlib)
))
(native-inputs ; for running tests
`(("perl" ,perl)
("which" ,which)
))
(build-system gnu-build-system)
(arguments
`(#:make-flags
(list
(string-append "EIGEN_INCLUDE_PATH="
(assoc-ref %build-inputs "eigen")
"/include/eigen3/")
"FORCE_DYNAMIC=1"
"DEBUG=1"
"fast-check"
)
#:phases
; "/include/eigen3/"
(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
#: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
mixed model and some of its close relatives for genome-wide
association studies (GWAS).")
(license license:gpl3))))
(define-public gemma-gn2
(package
(name "gemma")
(version "0.96")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
version ".tar.gz"))
(sha256
(base32
"055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))))
(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)))
(define-public gemma-wrapper
(package
(name "gemma-wrapper")
(version "0.92.2")
(source
(origin
(method url-fetch)
(uri (rubygems-uri "bio-gemma-wrapper" version))
(sha256
(base32
"08apz0imsxzwhzv2iicq2g5zx1iq1vlfrhk7khsfaydshbq5g741"))))
(build-system ruby-build-system)
(inputs `(("gemma-git-gn2" ,gemma-git-gn2)))
(arguments
`(#:tests? #f
#:phases
(modify-phases %standard-phases
(add-before
'build 'set-gemma-path
(lambda* (#:key outputs #:allow-other-keys)
(let ((out (assoc-ref outputs "out")))
(substitute* "bin/gemma-wrapper"
; (("gemma_command = ENV['GEMMA_COMMAND']")
(("gemma_command = ENV.*")
(string-append "gemma_command = '" (which "gemma") "'")))
))))))
(synopsis
"Gemma wrapper for LOCO and caching")
(description "Gemma wrapper")
(home-page "https://rubygems.org/gems/bio-gemma-wrapper")
(license license:gpl3)))
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