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authorpjotrp2017-09-03 07:11:57 +0000
committerpjotrp2017-09-03 07:11:57 +0000
commitda8185eedd20c3ba34d62d3134db559db8fed0f4 (patch)
tree252396ae9023c7d80c0ca7c9f557386076f10a19
parent92662274c27b447ee6874e9290ecd34fb36ab42c (diff)
downloadguix-bioinformatics-da8185eedd20c3ba34d62d3134db559db8fed0f4.tar.gz
gemma: updated wrapper to locate GEMMA
-rw-r--r--gn/packages/gemma.scm14
1 files changed, 8 insertions, 6 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index ef6c156..ff0a486 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -183,14 +183,14 @@ association studies (GWAS).")
(define-public gemma-wrapper
(package
(name "gemma-wrapper")
- (version "0.0.1")
+ (version "0.92.2")
(source
(origin
(method url-fetch)
(uri (rubygems-uri "bio-gemma-wrapper" version))
(sha256
(base32
- "16csqx5y63i5z0zkk1nq671n0vba482faskgsp1x1h75majqjdql"))))
+ "08apz0imsxzwhzv2iicq2g5zx1iq1vlfrhk7khsfaydshbq5g741"))))
(build-system ruby-build-system)
(inputs `(("gemma-git-gn2" ,gemma-git-gn2)))
(arguments
@@ -198,12 +198,14 @@ association studies (GWAS).")
#:phases
(modify-phases %standard-phases
(add-before
- 'install 'set-gemma-path
+ 'build 'set-gemma-path
(lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
+ (let ((out (assoc-ref outputs "out")))
(substitute* "bin/gemma-wrapper"
- (("GEMMA_COMMAND=options[:gemma_command]")
- (string-append "GEMMA_COMMAND=" (which "gemma"))))))))))
+ ; (("gemma_command = ENV['GEMMA_COMMAND']")
+ (("gemma_command = ENV.*")
+ (string-append "gemma_command = '" (which "gemma") "'")))
+ ))))))
(synopsis
"Gemma wrapper for LOCO and caching")
(description "Gemma wrapper")