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authorpjotrp2018-08-08 16:01:30 +0000
committerpjotrp2018-08-08 16:01:30 +0000
commitc4a0501c05a29f8272a058bcf8329aeb28136123 (patch)
tree86e30e89d1229c7f33bc81a479726729383980b0 /gn
parent99718d253ec9ed8ed836f0a348381a7cd83d4b9f (diff)
downloadguix-bioinformatics-c4a0501c05a29f8272a058bcf8329aeb28136123.tar.gz
Started on faster-lmm-dev package
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/gemma.scm101
1 files changed, 52 insertions, 49 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index e3a03c6..ba272f5 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -58,58 +58,9 @@
#: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 faster-lmm-d ; incomplete, just creates build environment
- (let ((commit "dea6abf61b633ed55e6a2997068f2d54abe5376b"))
- (package
- (name "faster-lmm-d")
- (version (string-append "0.0.1-" (string-take commit 7)))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/pjotrp/faster_lmm_d.git")
- (commit commit)))
- (file-name (string-append name "-" version "-checkout"))
- (sha256
- (base32
- "1syrn32g1q06bsnrk9wl7q2m5mvvglys2zl92rx0bi49kp2i0ngv"))))
- (build-system trivial-build-system)
- (propagated-inputs
- `(("openblas" ,openblas)
- ("gsl" ,gsl)
- ("lapack" ,lapack)
- ("dub" ,dub)
- ("gcc" ,gcc)
- ("glibc" ,glibc)
- ("binutils" ,binutils) ; for ld linker
- ("gfortran:lib" ,gfortran "lib")
- ; ("make" ,make)
- ))
- (native-inputs
- `(("ldc" ,ldc)
- ("shunit2" ,shunit2)
- ("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 "Parallel LMM")
- (description
- ".")
- (license license:gpl3))))
(define-public openblas-git
(let ((commit "893bd14e924fa72a4ed345a75d64c637f1b1c550"))
@@ -365,3 +316,55 @@ association studies (GWAS).")
(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))))