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authorPjotr Prins2018-01-29 11:30:28 +0000
committerPjotr Prins2018-01-29 11:30:28 +0000
commit06b203e722c0061aae6c16f877619dc7af03638e (patch)
treeac97f932deab04807bc4677843736791d70a0ebe
parent85316a82ec5df2c155f3c4d1dfd3739acf3d4145 (diff)
downloadgenenetwork2-06b203e722c0061aae6c16f877619dc7af03638e.tar.gz
Added checks in startup script, removed r-auwerx path
-rwxr-xr-xbin/genenetwork25
1 files changed, 4 insertions, 1 deletions
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