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authorpjotrp2017-08-29 09:50:21 +0000
committerpjotrp2017-08-29 09:50:21 +0000
commit967bb453503c6d7354a2e48b34dc36cefda3db5e (patch)
tree378bf986cd3888416bd62ce6992fd80e8d70c62a /gn
parent2ccf012475f3db74f6ea8ca496a1249ec7eb0508 (diff)
downloadguix-bioinformatics-967bb453503c6d7354a2e48b34dc36cefda3db5e.tar.gz
gemma-wrapper added
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/gemma.scm35
1 files changed, 28 insertions, 7 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 94433e2..2b6bba4 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -9,7 +9,7 @@
#: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 ruby)
#:use-module (guix build-system r)
#:use-module (guix build-system trivial)
#:use-module (gn packages statistics)
@@ -61,9 +61,9 @@
#:use-module (gn packages shell)
#:use-module (srfi srfi-1))
-(define-public gsl
+(define-public gsl1
(package
- (name "gsl")
+ (name "gsl1")
(version "1.16")
(source (origin
(method url-fetch)
@@ -86,19 +86,19 @@ numbers.")
(define-public gemma-git-gn2 ; guix candidate
- (let ((commit "48da44bf2da05f76008b083923ddf5701b9c029a"))
+ (let ((commit "ffc99d62013b1a5025b21cc385dd9892360ebe49"))
(package
(name "gemma-git-gn2")
- (version (string-append "0.97-gn2-" (string-take commit 7)))
+ (version (string-append "0.97.2-gn2-" (string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
- (url "https://github.com/genenetwork/GEMMA")
+ (url "https://github.com/genetics-statistics/GEMMA")
(commit commit)))
(file-name (string-append name "-" version))
(sha256
(base32
- "1bvf03aimk1nywv4z8dr75f2qi8mav346w787wzddckakn29yymb"))))
+ "0v68p469a5x8m0sdh408zbxc8gqb5ysqpp5hvh8h51sjf8lwyxv6"))))
(inputs `(
("gsl" ,gsl)
("eigen" ,eigen)
@@ -179,3 +179,24 @@ 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 "0.0.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (rubygems-uri "bio-gemma-wrapper" version))
+ (sha256
+ (base32
+ "16csqx5y63i5z0zkk1nq671n0vba482faskgsp1x1h75majqjdql"))))
+ (build-system ruby-build-system)
+ (propagated-inputs `(("gemma-git-gn2" ,gemma-git-gn2)))
+ (arguments
+ `(#:tests? #f))
+ (synopsis
+ "Gemma wrapper for LOCO and caching")
+ (description "Gemma wrapper")
+ (home-page "https://rubygems.org/gems/bio-gemma-wrapper")
+ (license license:gpl3)))