aboutsummaryrefslogtreecommitdiff
path: root/gn
diff options
context:
space:
mode:
authorpjotrp2017-08-24 09:18:08 +0000
committerpjotrp2017-08-24 09:18:08 +0000
commitedee34ded00e323231e362fd2a3d33b73949d2ab (patch)
treea10245134cf46c162ccb4b5b6a904909efe62577 /gn
parent66176c459477b479ac4cf7c9c83bec872e7ea0dc (diff)
parentffc2270004fccd6c0f9456891c99d91526bca1bf (diff)
downloadguix-bioinformatics-edee34ded00e323231e362fd2a3d33b73949d2ab.tar.gz
Conflict
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/gemma.scm18
-rw-r--r--gn/packages/genenetwork.scm8
-rw-r--r--gn/packages/phewas.scm9
3 files changed, 18 insertions, 17 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 67e8bf7..94433e2 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -61,7 +61,6 @@
#:use-module (gn packages shell)
#:use-module (srfi srfi-1))
-
(define-public gsl
(package
(name "gsl")
@@ -86,30 +85,30 @@ numbers.")
(license license:gpl3+)))
-(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)
))
@@ -121,6 +120,7 @@ numbers.")
(assoc-ref %build-inputs "eigen")
"/include/eigen3/")
"FORCE_DYNAMIC=1"
+ "DEBUG=1"
"WITH_OPENBLAS=1")
#:phases
; "/include/eigen3/"
@@ -143,7 +143,7 @@ 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..776a7d1 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)
@@ -152,7 +152,7 @@ location of a putative QTL.")
(let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd"))
(package
(name "genenetwork2")
- (version (string-append "2.10rc3-" (string-take commit 7) ))
+ (version (string-append "2.10rc4-" (string-take commit 7) ))
(source (origin
(method git-fetch)
(uri (git-reference
@@ -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")
diff --git a/gn/packages/phewas.scm b/gn/packages/phewas.scm
index 2bd832e..59269ef 100644
--- a/gn/packages/phewas.scm
+++ b/gn/packages/phewas.scm
@@ -19,6 +19,7 @@
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
+ #:use-module (gnu packages cran)
#:use-module (gnu packages file)
#:use-module (gnu packages gcc)
#:use-module (gnu packages java)
@@ -117,14 +118,14 @@ genome-wide association studies in structured populations.")
(define-public r-fgsea
(package
(name "r-fgsea")
- (version "1.0.2")
+ (version "1.2.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "fgsea" version))
(sha256
(base32
- "1yq4s4g4xxzcpkv9dpbg29444iy38vfgwj4wgr47rjjq8njfblfx"))))
+ "1vl9i889800avi8valkl0bz9jrjz71anzmal245ls9gwydrv0dpc"))))
(build-system r-build-system)
; (native-inputs
; `(("gfortran" ,gfortran)))
@@ -145,14 +146,14 @@ genome-wide association studies in structured populations.")
(define-public r-qvalue
(package
(name "r-qvalue")
- (version "2.6.0")
+ (version "2.8.0")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "qvalue" version))
(sha256
(base32
- "1dijh11v1kr29gnikq09pkdvm3qwmp1a406ahx9l4j6mgn8hlsfq"))))
+ "1dxdwa767a9r8n61r272ypi09qblcdfpzzwkmri74y5mbp1r3y4i"))))
(build-system r-build-system)
(propagated-inputs
`(("r-reshape2" ,r-reshape2)