diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/gemma.scm | 40 |
1 files changed, 35 insertions, 5 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm index 65aff46..ef6c156 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) @@ -86,19 +86,19 @@ numbers.") (define-public gemma-git-gn2 ; guix candidate - (let ((commit "be45bcca0ddc1d88066bd18a56ca57d588e41e99")) + (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 - "0gy7kqqcg4i7d16awh7hsd4ahwlvqsr35ab3yrzjr8faviy0r9hf")))) + "0v68p469a5x8m0sdh408zbxc8gqb5ysqpp5hvh8h51sjf8lwyxv6")))) (inputs `( ("gsl" ,gsl) ("eigen" ,eigen) @@ -179,3 +179,33 @@ 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) + (inputs `(("gemma-git-gn2" ,gemma-git-gn2))) + (arguments + `(#:tests? #f + #:phases + (modify-phases %standard-phases + (add-before + 'install 'set-gemma-path + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* "bin/gemma-wrapper" + (("GEMMA_COMMAND=options[:gemma_command]") + (string-append "GEMMA_COMMAND=" (which "gemma")))))))))) + (synopsis + "Gemma wrapper for LOCO and caching") + (description "Gemma wrapper") + (home-page "https://rubygems.org/gems/bio-gemma-wrapper") + (license license:gpl3))) |