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authorMuriithi Frederick Muriuki2018-08-03 10:06:31 +0300
committerMuriithi Frederick Muriuki2018-08-03 10:06:31 +0300
commitbfd171495846d6ced1988bb9a5a0de3daa5681a1 (patch)
treeb6ea3047d319df58822e1a7cb2f99c8a6f8965dd /gn/packages
parent486118be92bfc3953f3caf3645f746fa8d697e8d (diff)
parent99718d253ec9ed8ed836f0a348381a7cd83d4b9f (diff)
downloadguix-bioinformatics-bfd171495846d6ced1988bb9a5a0de3daa5681a1.tar.gz
Merge remote-tracking branch 'origin/master'
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/gemma.scm52
1 files changed, 52 insertions, 0 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 5e9b4b7..e3a03c6 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -31,6 +31,7 @@
#: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 ldc)
@@ -112,9 +113,11 @@
(define-public openblas-git
(let ((commit "893bd14e924fa72a4ed345a75d64c637f1b1c550"))
+ ; (let ((commit "36aea5ce2d5565e006a027a23e805cd9ff0e2eee"))
(package
(name "openblas-git")
(version (string-append "0.2.20-git-" (string-take commit 7)))
+ ; (version (string-append "0.3.1-git-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -124,6 +127,7 @@
(sha256
(base32
"0qv03c2yq46p9sajc3a3f56ijfifyv6f4n51a81wc2hihy4ilcap"))))
+ ; "1rva61y4lwi6zkja5349r59fxichdhqaqk608kklw5bwk04fjh86"))))
(build-system gnu-build-system)
(arguments
@@ -313,3 +317,51 @@ association studies (GWAS).")
(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))))