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authorpjotrp2017-05-18 10:14:32 +0000
committerpjotrp2017-05-18 10:14:32 +0000
commit774fcf1e81b820e4bb5e0ddd5db2edb37bb9ff4b (patch)
tree2604fb7b4e988784bfcbada82fed82057033a30b
parentb4b3302171d163342dbfaa1c80bd0874dcbddfc4 (diff)
downloadguix-bioinformatics-774fcf1e81b820e4bb5e0ddd5db2edb37bb9ff4b.tar.gz
Update gemma and remove overwrite of TWITTER_POST_FETCHER_JS_PATH - JS_PATH is standard now
-rw-r--r--gn/packages/gemma.scm4
-rw-r--r--gn/packages/genenetwork.scm4
2 files changed, 3 insertions, 5 deletions
diff --git a/gn/packages/gemma.scm b/gn/packages/gemma.scm
index 4ec2220..3c40317 100644
--- a/gn/packages/gemma.scm
+++ b/gn/packages/gemma.scm
@@ -107,14 +107,14 @@ association studies (GWAS).")
(define-public gemma
(package
(name "gemma")
- (version "0.95a") ; this build fails
+ (version "0.96")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/xiangzhou/GEMMA/archive/v"
version ".tar.gz"))
(sha256
(base32
- "1h0fqs45gy0n1nr76pzzagrv1cbcp7zaz34ljqb09jljc7c3lw9p"))))
+ "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222"))))
(inputs `(("gsl" ,gsl)
("lapack" ,lapack)
("zlib" ,zlib)))
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 63d687c..0e0d02e 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -199,7 +199,7 @@ location of a putative QTL.")
("r-wgcna" ,r-wgcna)
("redis" ,redis)
("mysql" ,mysql)
- ("gemma" ,gemma-git)
+ ("gemma" ,gemma)
("genenetwork2-files-small" ,genenetwork2-files-small)
("plink-ng" ,plink-ng)
("pylmm-gn2" ,pylmm-gn2)
@@ -239,7 +239,6 @@ location of a putative QTL.")
(lambda* (#:key inputs #:allow-other-keys)
(let* (
(datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" ))
- (twittercmd (string-append (assoc-ref inputs "javascript-twitter-post-fetcher") "/share/genenetwork2/javascript/Twitter-Post-Fetcher"))
(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"))
@@ -247,7 +246,6 @@ location of a putative QTL.")
(substitute* '("etc/default_settings.py")
(("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))
- (("^TWITTER_POST_FETCHER_JS_PATH =.*") (string-append "TWITTER_POST_FETCHER_JS_PATH = \"" twittercmd "\"\n" ))
(("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
(("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
(("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))