From 06b203e722c0061aae6c16f877619dc7af03638e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 29 Jan 2018 11:30:28 +0000
Subject: Added checks in startup script, removed r-auwerx path

---
 bin/genenetwork2 | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/bin/genenetwork2 b/bin/genenetwork2
index a7edb1c2..c6b08771 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -86,6 +86,9 @@ else
     export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis"
     export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma"
     export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper"
+    if [ ! -d $PYTHONPATH ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi
+    if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi
+    if [ ! -d $GEM_PATH ] ; then echo "GEM_PATH not valid "$GEM_PATH ; exit 1 ; fi
 fi
 if [ -z $PYTHONPATH ] ; then
     echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!"
@@ -127,7 +130,7 @@ dbfilename gn2.rdb
 " | redis-server - &
 
 # Overrides for packages that are not yet public (currently r-auwerx)
-export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
+# export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
 
 # Start the flask server running GN2
 cd $GN2_BASE_DIR/wqflask
-- 
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