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| author | Pjotr Prins | 2017-08-22 05:21:51 -0500 |
|---|---|---|
| committer | Pjotr Prins | 2017-08-22 05:21:51 -0500 |
| commit | f643ef8969455a17e382ec4bc8e48e27e5a95957 (patch) | |
| tree | 5d180ca5afdb0596f5ec38ec13a43f12a2b96b28 /gn/packages | |
| parent | e50493dc409464bacaa06775418c32be3f1aacf5 (diff) | |
| download | guix-bioinformatics-f643ef8969455a17e382ec4bc8e48e27e5a95957.tar.gz | |
Updated gemma to latest
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/gemma.scm | 17 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 6 |
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") |