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authorPjotr Prins2017-08-22 05:21:51 -0500
committerPjotr Prins2017-08-22 05:21:51 -0500
commitf643ef8969455a17e382ec4bc8e48e27e5a95957 (patch)
tree5d180ca5afdb0596f5ec38ec13a43f12a2b96b28 /gn
parente50493dc409464bacaa06775418c32be3f1aacf5 (diff)
downloadguix-bioinformatics-f643ef8969455a17e382ec4bc8e48e27e5a95957.tar.gz
Updated gemma to latest
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/gemma.scm17
-rw-r--r--gn/packages/genenetwork.scm6
2 files changed, 12 insertions, 11 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 69607b3..a1481cb 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -61,30 +61,30 @@
#:use-module (gn packages shell)
#:use-module (srfi srfi-1))
-(define-public gemma-git ; guix candidate
- (let ((commit "c91dfaef84d08ce151eecca50bf8ffdaf4b327f6"))
+(define-public gemma-git-gn2 ; guix candidate
+ (let ((commit "48da44bf2da05f76008b083923ddf5701b9c029a"))
(package
- (name "gemma-git")
- (version (string-append "0.97-pre-" (string-take commit 7)))
+ (name "gemma-git-gn2")
+ (version (string-append "0.97-gn2-" (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 "-" commit))
+ (file-name (string-append name "-" version))
(sha256
(base32
- "1ix4p6av88i6jfv84v2qqcmdlnxznp64bm93avrrl68v04jq6psm"))))
+ "1bvf03aimk1nywv4z8dr75f2qi8mav346w787wzddckakn29yymb"))))
(inputs `(
("gsl" ,gsl)
("eigen" ,eigen)
+ ("shunit2" ,shunit2)
("lapack" ,lapack)
("openblas" ,openblas)
("zlib" ,zlib)
))
(native-inputs ; for running tests
`(("perl" ,perl)
- ("shunit2" ,shunit2)
("which" ,which)
))
@@ -96,6 +96,7 @@
(assoc-ref %build-inputs "eigen")
"/include/eigen3/")
"FORCE_DYNAMIC=1"
+ "DEBUG=1"
"WITH_OPENBLAS=1")
#:phases
; "/include/eigen3/"
@@ -118,7 +119,7 @@ mixed model and some of its close relatives for genome-wide
association studies (GWAS).")
(license license:gpl3))))
-(define-public gemma
+(define-public gemma-gn2
(package
(name "gemma")
(version "0.96")
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index b55c37f..ea7fcd6 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -44,7 +44,7 @@
#:use-module (gnu packages bootstrap)
#:use-module (gnu packages version-control)
#:use-module (gn packages bioinformatics)
- ; #:use-module (gn packages gemma)
+ #:use-module (gn packages gemma)
#:use-module (gn packages javascript)
#:use-module (gn packages phewas)
#:use-module (gn packages python)
@@ -175,7 +175,7 @@ location of a putative QTL.")
("r-wgcna" ,r-wgcna)
("redis" ,redis)
("mysql" ,mysql)
- ("gemma" ,gemma)
+ ("gemma-git-gn2" ,gemma-git-gn2)
("genenetwork2-files-small" ,genenetwork2-files-small)
("plink-ng" ,plink-ng)
("pylmm-gn2" ,pylmm-gn2)
@@ -233,7 +233,7 @@ 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") "/bin/plink2"))
- (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
+ (gemmacmd (string-append (assoc-ref inputs "gemma-git-gn2") "/bin/gemma"))
)
(substitute* '("etc/default_settings.py")