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authorpjotrp2020-11-21 10:43:24 +0000
committerpjotrp2020-11-21 10:43:52 +0000
commit8a66ab55cab786acb9cba38b387bbbc58fa35dfa (patch)
treec573456e1e984d49c595370527ba871da58d323f /gn
parentf129c4fc90fd70b6a468537bda8c497f2bee2277 (diff)
downloadguix-bioinformatics-8a66ab55cab786acb9cba38b387bbbc58fa35dfa.tar.gz
Updated CWL
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/gemma.scm60
1 files changed, 59 insertions, 1 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 9bbb186..e6d49b4 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -100,7 +100,7 @@
(license license:bsd-3))))
-(define-public gemma-gn2 ; guix candidate - generic openblas version
+(define-public gemma-gn2 ; Version used in GeneNetwork. Guix candidate - generic openblas version
(let ((commit "97547ee82e0bd1cc2210612415b0ceb135dbba6d"))
(package
(name "gemma-gn2")
@@ -176,6 +176,63 @@ genome-wide association studies (GWAS).")
#:parallel-tests? #f))
))
+(define-public gemma-gn2-dev ; Dev version for GeneNetwork. Not a Guix candidate
+ (let ((commit "d53a04edc476d820de7a611cacc8b105115aa3cc"))
+ (package
+ (name "gemma-gn2-dev")
+ (version (string-append "0.98.2-" (string-take commit 7)))
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/genenetwork/GEMMA")
+ (commit commit)))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "0xm4cjfzrcb1wc8lw9p1727spica8rlzwnvjkp7ackn1g7zmzhw0"))))
+ ; guix environment -C guix --ad-hoc gcc-toolchain gdb gsl openblas zlib bash ld-wrapper perl vim which
+ (inputs `(
+ ("gsl" ,gsl)
+ ("shunit2" ,shunit2)
+ ("openblas" ,openblas)
+ ("zlib" ,zlib)
+ ))
+ (native-inputs ; for running tests
+ `(("perl" ,perl)
+ ("which" ,which)
+ ))
+
+ (build-system gnu-build-system)
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (add-before 'build 'bin-mkdir
+ (lambda _
+ (mkdir-p "bin")
+ ))
+ (replace 'build
+ (lambda* (#:key inputs #:allow-other-keys)
+ (invoke "make" "debug" "-j" (number->string (parallel-job-count)))))
+ (replace 'check
+ (lambda* (#:key inputs #:allow-other-keys)
+ (invoke "make" "fast-check" )))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ (install-file "bin/gemma" (string-append out "/bin"))))))
+ ; #:tests? #f
+ #:parallel-tests? #f))
+ (home-page "http://www.xzlab.org/software.html")
+ (synopsis "Tool for genome-wide efficient mixed model association")
+ (description "Genome-wide Efficient Mixed Model Association (GEMMA)
+provides a standard linear mixed model resolver with application in
+genome-wide association studies (GWAS).")
+
+ (license license:gpl3))))
+
+
+
(define-public gemma-wrapper
(package
(name "gemma-wrapper")
@@ -256,6 +313,7 @@ genome-wide association studies (GWAS).")
(description "Gemma-development")
(license license:gpl3))))
+
(define-public faster-lmm-d-dev ; incomplete, just creates build environment
(let ((commit "68e22043ce0ca348cbc4f3bdd015e036ba9ac5f2"))
(package