(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 gdb) #:use-module (gnu packages graphviz) #:use-module (gnu packages java) #:use-module (gnu packages dlang) #: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 shell) #:use-module (srfi srfi-1)) (define-public openblas-git (let ((commit "2263d3906c23bd7341ebe714ef7c44fc84b0d1d0")) (package (name "openblas-git") (version (string-append "0.3.3-git-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/xianyi/OpenBLAS.git") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "1x2axq36szcz1gc77vcf3ypm0g1r3jwj03vq6rr94h098rcdv4s9")))) (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))) ; BINARY=64 NO_WARMUP=0 GEMM_MULTITHREAD_THRESHOLD=4 USE_THREAD=1 NO_AFFINITY=0 NO_LAPACK=0 NUM_THREADS=64 #: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=0" ; use OpenBlas LAPACK "COMMON_PROF=0" ; disable profiling "DEBUG=0" ;; Build the library for all supported CPUs. This allows ;; switching CPU targets at runtime with the environment variable ;; OPENBLAS_CORETYPE=, 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)) ((string-prefix? "x86_64" system) '("DYNAMIC_ARCH=1")) ;; 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 "Platform 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 gemma-gn2 ; guix candidate - generic openblas version (let ((commit "6b1e007ea9ead6123e9d7f078f3e59054047521d")) (package (name "gemma-gn2") (version (string-append "0.98-" (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 "0gg4rrxcjbhfqfdaljnn86yffaa0n2d2j67j2gv47wvgrnn8fvwz")))) (inputs `( ; ("gfortran:lib" ,gfortran "lib") ("gsl" ,gsl) ("eigen" ,eigen) ("shunit2" ,shunit2) ; ("lapack" ,lapack) ("openblas" ,openblas) ("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/") ) #: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 "Genome-wide Efficient Mixed Model Association (GEMMA) provides a standard linear mixed model resolver with application in genome-wide association studies (GWAS).") (license license:gpl3)))) (define-public gemma-gn2-git ; openblas optimized (package (inherit gemma-gn2) (name "gemma-gn2-git") (inputs `( ; ("gfortran:lib" ,gfortran "lib") ("gsl" ,gsl) ("eigen" ,eigen) ("shunit2" ,shunit2) ("openblas" ,openblas-git) ("zlib" ,zlib) )) (arguments `(#:make-flags (list (string-append "EIGEN_INCLUDE_PATH=" (assoc-ref %build-inputs "eigen") "/include/eigen3/") ) #: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)) )) (define-public gemma-wrapper (package (name "gemma-wrapper") (version "0.98.1") (source (origin (method url-fetch) (uri (rubygems-uri "bio-gemma-wrapper" version)) (sha256 (base32 "0wysg7s64vyzm19j2hvxyflbszx00d9diw9zwzbqirzagzmqbfwk")))) (build-system ruby-build-system) (inputs `(("gemma-gn2" ,gemma-gn2-git))) (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))) (define-public gemma-dev-env (let ((md5 "93e745e9c")) (package (name "gemma-dev-env") (version "0.98") (source (origin (method url-fetch) (uri "http://biogems.info/genenetwork2-2.0-a8fcff4.svg") ; any old file (file-name (string-append name "-" md5)) (sha256 (base32 "0rir1mcn3a8i1mbw3ppgnjl7wg71mapljik7n3v5i8j5ic95mqr5")))) (build-system trivial-build-system) (native-inputs `(("unzip" ,unzip) ("source" ,source))) (inputs `(("sassc" ,sassc))) (propagated-inputs `(("binutils" ,binutils) ; for ld ("gemma-gn2" ,gemma-gn2-git) ; ("gemma-wrapper" ,gemma-wrapper) ("gcc" ,gcc-7) ("gdb" ,gdb) ("gfortran:lib" ,gfortran "lib") ("glibc" ,glibc) ; for crt1.o ("gsl" ,gsl) ("eigen" ,eigen) ("linux-libre-headers" ,linux-libre-headers) ("openblas" ,openblas-git) ("shunit2" ,shunit2) ("zlib" ,zlib) )) (arguments `(#:modules ((guix build utils)) #:builder (begin (use-modules (guix build utils)) (let ((target (string-append (assoc-ref %outputs "out") "/share"))) (write target) (mkdir-p target) ; (copy-recursively (assoc-ref %build-inputs "source") target) #t)))) (home-page "http://github.com/genetics-statistics/") (synopsis "GEMMA development environment imports build tools, gemma-wrapper and faster-lmm-d") (description "Gemma-development") (license license:gpl3)))) (define-public faster-lmm-d-dev ; incomplete, just creates build environment (let ((commit "68e22043ce0ca348cbc4f3bdd015e036ba9ac5f2")) (package (name "faster-lmm-d-dev") (version (string-append "0.0.1-" (string-take commit 7))) (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/genetics-statistics/faster_lmm_d.git") (commit commit))) (file-name (string-append name "-" version "-checkout")) (sha256 (base32 "0awcsrmpq1zbcy145l5ssmsxzfq5dq9yr0901hk977lmjf99gxng")))) (build-system trivial-build-system) (propagated-inputs `(("openblas" ,openblas) ("gsl" ,gsl) ; ("lapack" ,lapack) ("dub" ,dub) ("gcc" ,gcc-7) ("gdb" ,gdb) ; ("glibc" ,glibc) ("binutils" ,binutils) ; for ld linker ("gfortran:lib" ,gfortran "lib") ; ("make" ,make) ("ldc" ,ldc) ("shunit2" ,shunit2) ("linux-libre-headers" ,linux-libre-headers) ("openblas" ,openblas-git) )) (inputs `( ("which" ,which) )) (arguments `(#:modules ((guix build utils)) #:builder (begin (use-modules (guix build utils)) (let ((target (string-append (assoc-ref %outputs "out") "/share"))) (write target) (mkdir-p target) ; (copy-recursively (assoc-ref %build-inputs "source") target) #t)))) (home-page "https://github.com/pjotrp") (synopsis "Build system for faster-lmm-d") (description ".") (license license:gpl3))))