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@ -23,101 +23,23 @@ |
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#:use-module (srfi srfi-1)) |
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(define-public openblas-git |
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(let ((commit "63b03efc2af332c88b86d4fd8079d00f4b439adf")) |
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(package |
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(name "openblas-git") |
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(version (string-append "0.3.10-git-" (string-take commit 7))) |
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(source (origin |
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(method git-fetch) |
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(uri (git-reference |
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(url "https://github.com/xianyi/OpenBLAS.git") |
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(commit commit))) |
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(file-name (string-append name "-" version "-checkout")) |
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(sha256 |
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(base32 |
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"174id98ga82bhz2v7sy9yj6pqy0h0088p3mkdikip69p9rh3d17b")))) |
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(build-system gnu-build-system) |
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(arguments |
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`( |
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#:tests? #f ;no "check" target |
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;; DYNAMIC_ARCH is only supported on x86. When it is disabled and no |
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;; TARGET is specified, OpenBLAS will tune itself to the build host, so |
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;; we need to disable substitutions. |
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#:substitutable? |
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,(let ((system (or (%current-target-system) (%current-system)))) |
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(or (string-prefix? "x86_64" system) |
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(string-prefix? "i686" system) |
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(string-prefix? "mips" system) |
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(string-prefix? "aarch64" system))) |
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; BINARY=64 NO_WARMUP=0 GEMM_MULTITHREAD_THRESHOLD=4 USE_THREAD=1 NO_AFFINITY=0 NO_LAPACK=0 NUM_THREADS=64 |
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#:make-flags |
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(list (string-append "PREFIX=" (assoc-ref %outputs "out")) |
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"SHELL=bash" |
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"NUM_THREADS=64" |
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"BINARY=64" |
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"NO_WARMUP=0" |
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"GEMM_MULTITHREAD_THRESHOLD=4" |
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"USE_THREAD=1" |
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"NO_AFFINITY=0" |
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"NO_LAPACK=0" ; use OpenBlas LAPACK |
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"COMMON_PROF=0" ; disable profiling |
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"DEBUG=0" |
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;; Build the library for all supported CPUs. This allows |
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;; switching CPU targets at runtime with the environment variable |
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;; OPENBLAS_CORETYPE=<type>, where "type" is a supported CPU type. |
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;; Unfortunately, this is not supported on non-x86 architectures, |
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;; where it leads to failed builds. |
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,@(let ((system (or (%current-target-system) (%current-system)))) |
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(cond |
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; ((or (string-prefix? "x86_64" system) |
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; (string-prefix? "i686" system)) |
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((string-prefix? "x86_64" system) |
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'("DYNAMIC_ARCH=1")) |
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;; On MIPS we force the "SICORTEX" TARGET, as for the other |
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;; two available MIPS targets special extended instructions |
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;; for Loongson cores are used. |
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((string-prefix? "mips" system) |
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'("TARGET=SICORTEX")) |
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;; On aarch64 force the generic 'armv8-a' target |
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((string-prefix? "aarch64" system) |
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'("TARGET=ARMV8")) |
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(else '())))) |
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;; no configure script |
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#:phases (alist-delete 'configure %standard-phases))) |
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(inputs |
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`(("gfortran" ,gfortran) |
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("gfortran:lib" ,gfortran "lib"))) |
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(native-inputs |
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`(("cunit" ,cunit) |
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("perl" ,perl))) |
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(home-page "http://www.openblas.net/") |
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(synopsis "Platform optimized BLAS library based on GotoBLAS") |
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(description |
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"OpenBLAS is a BLAS library forked from the GotoBLAS2-1.13 BSD version.") |
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(license license:bsd-3)))) |
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;; See also the recent gemma.scm in the GEMMA repo! |
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(define-public gemma-gn2 ; guix candidate - currently uses generic |
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; openblas version and genenetwork github repo |
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(let ((commit "47221d6e9891bf9b20ce6e1e909856ccb0ae575f")) |
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(let ((commit "140667153f7ad601af2761e0856c396ce2808a78")) |
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(package |
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(name "gemma-gn2") |
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(version (string-append "0.98.3-" (string-take commit 7))) |
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(version (string-append "0.98.4-" (string-take commit 7))) |
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(source (origin |
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(method git-fetch) |
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(uri (git-reference |
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(url "https://github.com/genenetwork/GEMMA") |
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(url "https://github.com/genenetwork/GEMMA") |
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(commit commit))) |
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(file-name (string-append name "-" version "-checkout")) |
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(sha256 |
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(base32 |
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"0wydfm2svrlrz4zbrvxymqc33ici3vi7xy9br37mfbb9lh3fmb2w")))) |
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"0km2m3xhq8a5d6nv7n9r0jmxhc2fy8f3q88mfqarmcqybbyplsd4")))) |
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(inputs `( |
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("gsl" ,gsl) |
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("shunit2-old" ,shunit2-old) |
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@ -152,14 +74,16 @@ genome-wide association studies (GWAS).") |
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(license license:gpl3)))) |
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(define-public gemma-gn2-git ; openblas optimized |
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(define-public gemma-gn2-git ; typically use latest for genenetwork, |
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; may switch off tests and (maybe) |
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; openblas optimized |
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(package |
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(inherit gemma-gn2) |
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(name "gemma-gn2-git") |
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(inputs `( |
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("gsl" ,gsl) |
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("shunit2-old" ,shunit2-old) |
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("openblas" ,openblas-git) |
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("openblas" ,openblas) |
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("zlib" ,zlib) |
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)) |
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(arguments |
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@ -179,62 +103,6 @@ genome-wide association studies (GWAS).") |
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#:parallel-tests? #f)) |
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)) |
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(define-public gemma-gn2-dev ; Dev version for GeneNetwork. Not a Guix candidate |
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(let ((commit "8524ca2c6c0e1ee0f92091e4af7ee71e87654cc2")) |
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(package |
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(name "gemma-gn2-dev") |
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(version (string-append "0.98.4-" (string-take commit 7))) |
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(source (origin |
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(method git-fetch) |
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(uri (git-reference |
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(url "https://github.com/genenetwork/GEMMA") |
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(commit commit))) |
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(file-name (string-append name "-" version "-checkout")) |
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(sha256 |
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(base32 |
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"0fn7yj1dgfhk178i096al5d3z5xmsz5krl9mf9v3xn4ima4ak7q3")))) |
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; guix environment -C guix --ad-hoc gcc-toolchain gdb gsl openblas zlib bash ld-wrapper perl vim which |
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(inputs `( |
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("gsl" ,gsl) |
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("shunit2-old" ,shunit2-old) |
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("openblas" ,openblas) |
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("zlib" ,zlib) |
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)) |
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(native-inputs ; for running tests |
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`(("perl" ,perl) |
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("which" ,which) |
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)) |
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(build-system gnu-build-system) |
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(arguments |
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`(#:phases |
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(modify-phases %standard-phases |
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(delete 'configure) |
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(add-before 'build 'bin-mkdir |
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(lambda _ |
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(mkdir-p "bin") |
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)) |
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(replace 'build |
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(lambda* (#:key inputs #:allow-other-keys) |
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(invoke "make" "debug" "-j" (number->string (parallel-job-count))))) |
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(replace 'check |
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(lambda* (#:key inputs #:allow-other-keys) |
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(invoke "make" "fast-check" ))) |
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(replace 'install |
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(lambda* (#:key outputs #:allow-other-keys) |
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(let ((out (assoc-ref outputs "out"))) |
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(install-file "bin/gemma" (string-append out "/bin")))))) |
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; #:tests? #f |
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#:parallel-tests? #f)) |
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(home-page "http://www.xzlab.org/software.html") |
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(synopsis "Tool for genome-wide efficient mixed model association") |
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(description "Genome-wide Efficient Mixed Model Association (GEMMA) |
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provides a standard linear mixed model resolver with application in |
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genome-wide association studies (GWAS).") |
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(license license:gpl3)))) |
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(define-public gemma-wrapper |
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(package |
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@ -270,104 +138,3 @@ genome-wide association studies (GWAS).") |
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(description "Gemma wrapper") |
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(home-page "https://rubygems.org/gems/bio-gemma-wrapper") |
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(license license:gpl3))) |
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(define-public gemma-dev-env |
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(let ((md5 "93e745e9c")) |
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(package |
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(name "gemma-dev-env") |
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(version "0.98") |
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(source |
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(origin |
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(method url-fetch) |
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(uri "http://biogems.info/genenetwork2-2.0-a8fcff4.svg") ; any old file |
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(file-name (string-append name "-" md5)) |
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(sha256 |
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(base32 "0rir1mcn3a8i1mbw3ppgnjl7wg71mapljik7n3v5i8j5ic95mqr5")))) |
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(build-system trivial-build-system) |
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(native-inputs `(("unzip" ,unzip) |
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("source" ,source))) |
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(inputs `(("sassc" ,sassc))) |
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(propagated-inputs |
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`(("binutils" ,binutils) ; for ld |
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("gemma-gn2" ,gemma-gn2-git) |
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; ("gemma-wrapper" ,gemma-wrapper) |
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("gcc" ,gcc-7) |
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("gdb" ,gdb) |
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("gfortran:lib" ,gfortran "lib") |
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("glibc" ,glibc) ; for crt1.o |
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("gsl" ,gsl) |
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("eigen" ,eigen) |
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("linux-libre-headers" ,linux-libre-headers) |
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("openblas" ,openblas-git) |
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("shunit2-old" ,shunit2-old) |
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("zlib" ,zlib) |
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)) |
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(arguments |
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`(#:modules ((guix build utils)) |
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#:builder |
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(begin |
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(use-modules (guix build utils)) |
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(let ((target (string-append (assoc-ref %outputs "out") |
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"/share"))) |
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(write target) |
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(mkdir-p target) |
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; (copy-recursively (assoc-ref %build-inputs "source") target) |
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#t)))) |
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(home-page "http://github.com/genetics-statistics/") |
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(synopsis "GEMMA development environment imports build tools, gemma-wrapper and faster-lmm-d") |
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(description "Gemma-development") |
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(license license:gpl3)))) |
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(define-public faster-lmm-d-dev ; incomplete, just creates build environment |
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(let ((commit "68e22043ce0ca348cbc4f3bdd015e036ba9ac5f2")) |
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(package |
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(name "faster-lmm-d-dev") |
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(version (string-append "0.0.1-" (string-take commit 7))) |
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(source (origin |
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(method git-fetch) |
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(uri (git-reference |
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(url "https://github.com/genetics-statistics/faster_lmm_d.git") |
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(commit commit))) |
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(file-name (string-append name "-" version "-checkout")) |
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(sha256 |
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(base32 |
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"0awcsrmpq1zbcy145l5ssmsxzfq5dq9yr0901hk977lmjf99gxng")))) |
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(build-system trivial-build-system) |
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(propagated-inputs |
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`(("openblas" ,openblas) |
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("gsl" ,gsl) |
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; ("lapack" ,lapack) |
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("dub" ,dub) |
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("gcc" ,gcc-7) |
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("gdb" ,gdb) |
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; ("glibc" ,glibc) |
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("binutils" ,binutils) ; for ld linker |
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("gfortran:lib" ,gfortran "lib") |
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; ("make" ,make) |
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("ldc" ,ldc) |
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("shunit2-old" ,shunit2-old) |
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("linux-libre-headers" ,linux-libre-headers) |
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("openblas" ,openblas-git) |
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)) |
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(inputs |
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`( |
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("which" ,which) |
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)) |
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(arguments |
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`(#:modules ((guix build utils)) |
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#:builder |
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(begin |
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(use-modules (guix build utils)) |
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(let ((target (string-append (assoc-ref %outputs "out") |
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"/share"))) |
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(write target) |
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(mkdir-p target) |
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; (copy-recursively (assoc-ref %build-inputs "source") target) |
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#t)))) |
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(home-page "https://github.com/pjotrp") |
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(synopsis "Build system for faster-lmm-d") |
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(description |
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".") |
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(license license:gpl3)))) |
pjotrp
11 months ago