From 8145507d6d617554cf996e6cebf286d30ae64df0 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 4 Apr 2018 16:58:21 +0000
Subject: ES: doc

---
 bin/genenetwork2 | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

(limited to 'bin')

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
-- 
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