From 774fcf1e81b820e4bb5e0ddd5db2edb37bb9ff4b Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Thu, 18 May 2017 10:14:32 +0000
Subject: Update gemma and remove overwrite of TWITTER_POST_FETCHER_JS_PATH -
 JS_PATH is standard now

---
 gn/packages/gemma.scm       | 4 ++--
 gn/packages/genenetwork.scm | 4 +---
 2 files changed, 3 insertions(+), 5 deletions(-)

(limited to 'gn')

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" ))
-- 
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