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-rwxr-xr-xbin/genenetwork218
1 files changed, 12 insertions, 6 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 3f06e7f9..18e02388 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -21,10 +21,18 @@
#
# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_settings.py
#
-# To run a maintenance script with settings (instead of the webserver) add that with
-# a -c switch, e.g.
+# To run a maintenance python script with settings (instead of the
+# webserver) add that with a -c switch, e.g.
#
-# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py
+# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 -c ./wqflask/maintenance/gen_select_dataset.py
+#
+# To run any script in the environment
+#
+# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD"
+#
+# To get a python REPL(!)
+#
+# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -cli python
#
# For development you may want to run
#
@@ -114,7 +122,6 @@ else
export PATH=$GN2_PROFILE/bin:$PATH
export PYTHONPATH="$GN2_PROFILE/lib/python2.7/site-packages" # never inject another PYTHONPATH!!
export R_LIBS_SITE=$GN2_PROFILE/site-library
- export GEM_PATH=$GN2_PROFILE/lib/ruby/gems/2.4.0
export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript
export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0"
export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0"
@@ -134,7 +141,6 @@ else
done
done <<< "$PYTHONPATH"
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!"
@@ -170,9 +176,9 @@ if [ "$1" = '-c' ] ; then
python $cmd $*
exit $?
fi
+
# Now handle command parameter -cli which runs in bash
if [ "$1" = "-cli" ] ; then
- echo "HERE"
cd $GN2_BASE_DIR/wqflask
cmd=$2
echo PYTHONPATH=$PYTHONPATH