diff options
Diffstat (limited to 'bin/genenetwork2')
| -rwxr-xr-x | bin/genenetwork2 | 18 |
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 |