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authorpjotrp2017-12-27 10:24:27 +0000
committerpjotrp2017-12-27 10:24:27 +0000
commited093776afcb33d1601e9390e0458fd0f782fc99 (patch)
treec33a41c2d00be6182be59f1bd8432f292734f960
parent9df032aa61bb669faf49fbadaf86d7319bf2801b (diff)
downloadguix-bioinformatics-ed093776afcb33d1601e9390e0458fd0f782fc99.tar.gz
gemma: provide generic package
-rw-r--r--gn/packages/gemma.scm60
-rw-r--r--gn/packages/genenetwork.scm4
2 files changed, 21 insertions, 43 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 803d592..fb9e2c7 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -139,7 +139,7 @@
(license license:bsd-3))))
-(define-public gsl1 ; supporting older GSL tests
+(define-public gsl1 ; supporting older GSL tests - no longer really used
(package
(name "gsl1")
(version "1.16")
@@ -163,10 +163,10 @@ numbers.")
(license license:gpl3+)))
-(define-public gemma-git-gn2 ; guix candidate
+(define-public gemma-gn2 ; guix candidate - generic openblas version
(let ((commit "c760aa09c2aa91ca6270b5f898c27e9aed376a73"))
(package
- (name "gemma-git-gn2")
+ (name "gemma-gn2")
(version (string-append "0.97-" (string-take commit 7)))
(source (origin
(method git-fetch)
@@ -182,8 +182,8 @@ numbers.")
("gsl" ,gsl)
("eigen" ,eigen)
("shunit2" ,shunit2)
- ; ("lapack" ,lapack) - included in openblas-haswell
- ("openblas" ,openblas-haswell)
+ ("lapack" ,lapack)
+ ("openblas" ,openblas)
("zlib" ,zlib)
))
(native-inputs ; for running tests
@@ -198,6 +198,7 @@ numbers.")
(string-append "EIGEN_INCLUDE_PATH="
(assoc-ref %build-inputs "eigen")
"/include/eigen3/")
+ "WITH_LAPACK=1"
)
#:phases
; "/include/eigen3/"
@@ -221,42 +222,19 @@ mixed model and some of its close relatives for genome-wide
association studies (GWAS).")
(license license:gpl3))))
-(define-public gemma-gn2
+(define-public gemma-gn2-haswell ; openblas optimized for haswell
(package
- (name "gemma")
- (version "0.96")
- (source (origin
- (method url-fetch)
- (uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
- version ".tar.gz"))
- (sha256
- (base32
- "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))))
- (inputs `(("gsl" ,gsl)
- ("lapack" ,lapack)
- ("zlib" ,zlib)))
- (build-system gnu-build-system)
- (arguments
- `(#:make-flags '("FORCE_DYNAMIC=1")
- #:phases
- (modify-phases %standard-phases
- (delete 'configure)
- (add-before 'build 'bin-mkdir
- (lambda _
- (mkdir-p "bin")
- ))
- (replace 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- (install-file "bin/gemma" (string-append out "/bin"))))))
- #:tests? #f)) ; no tests included
- (home-page "")
- (synopsis "Tool for genome-wide efficient mixed model association")
- (description "GEMMA is software implementing the Genome-wide
-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)))
+ (inherit gemma-gn2)
+ (name "gemma-gn2-haswell")
+ (inputs `(
+ ("gfortran:lib" ,gfortran "lib")
+ ("gsl" ,gsl)
+ ("eigen" ,eigen)
+ ("shunit2" ,shunit2)
+ ("openblas" ,openblas-haswell)
+ ("zlib" ,zlib)
+ ))
+ ))
(define-public gemma-wrapper
(package
@@ -270,7 +248,7 @@ association studies (GWAS).")
(base32
"08apz0imsxzwhzv2iicq2g5zx1iq1vlfrhk7khsfaydshbq5g741"))))
(build-system ruby-build-system)
- (inputs `(("gemma-git-gn2" ,gemma-git-gn2)))
+ (inputs `(("gemma-gn2" ,gemma-gn2-haswell)))
(arguments
`(#:tests? #f
#:phases
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 52d2dce..479f694 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -192,7 +192,7 @@ location of a putative QTL.")
("r-wgcna" ,r-wgcna)
("redis" ,redis)
("mysql" ,mysql)
- ("gemma-git-gn2" ,gemma-git-gn2)
+ ("gemma" ,gemma-gn2-haswell)
("gemma-wrapper" ,gemma-wrapper)
("genenetwork2-files-small" ,genenetwork2-files-small)
("plink-ng-gn" ,plink-ng-gn)
@@ -252,7 +252,7 @@ location of a putative QTL.")
(datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" ))
(pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
(plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
- (gemmacmd (string-append (assoc-ref inputs "gemma-git-gn2") "/bin/gemma"))
+ (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
)
(substitute* '("etc/default_settings.py")