diff options
| -rw-r--r-- | README.md | 4 | ||||
| -rwxr-xr-x | bin/genenetwork2 | 34 |
2 files changed, 0 insertions, 38 deletions
diff --git a/README.md b/README.md index d5539a9f..8dcbac9e 100644 --- a/README.md +++ b/README.md @@ -46,10 +46,6 @@ Also mariadb and redis need to be running, see ## Development -It may be useful to pull in the GN3 python modules locally. For this -use `GN3_PYTHONPATH` environment that gets injected in -the ./bin/genenetwork2 startup. - ## Testing To have tests pass, the redis and mariadb instance should be running, because of diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 93ab02f8..934a10d8 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -91,14 +91,7 @@ fi export GN2_SETTINGS=$settings # Python echo GN2_SETTINGS=$settings -export PATH=$GN2_PROFILE/bin:$PATH -export PYTHONPATH="$GN2_PROFILE/lib/python3.8/site-packages" # never inject another PYTHONPATH!! -export R_LIBS_SITE=$GN2_PROFILE/site-library export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript -export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0" -export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0" -export XDG_DATA_DIRS="$GN2_PROFILE/share" -export GIO_EXTRA_MODULES="$GN2_PROFILE/lib/gio/modules" export LC_ALL=C # FIXME export GUIX_GENENETWORK_FILES="$GN2_PROFILE/share/genenetwork2" export PLINK_COMMAND="$GN2_PROFILE/bin/plink2" @@ -106,25 +99,6 @@ export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma" if [ -z $GEMMA_WRAPPER_COMMAND ]; then export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper" fi -while IFS=":" read -ra PPATH; do - for PPART in "${PPATH[@]}"; do - if [ ! -d $PPART ] ; then echo "$PPART in PYTHONPATH not valid $PYTHONPATH" ; exit 1 ; fi - done -done <<< "$PYTHONPATH" -if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi -if [ -z $PYTHONPATH ] ; then - echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!" - exit 1 -fi -if [ ! -d $R_LIBS_SITE ] ; then - echo "ERROR R_LIBS_SITE has not been set correctly (we only allow one path) - use GN2_PROFILE!" - echo "Paste into your shell the output of (for example)" - echo "guix package -p \$GN2_PROFILE --search-paths" - exit 1 -fi - -# We may change this one: -export PYTHONPATH=$PYTHON_GN_PATH:$GN2_BASE_DIR/wqflask:$GN3_PYTHONPATH:$PYTHONPATH # Our UNIX TMPDIR defaults to /tmp - change this on a shared server if [ -z $TMPDIR ]; then @@ -140,7 +114,6 @@ set|grep TMPDIR if [ "$1" = '-c' ] ; then cd $GN2_BASE_DIR/wqflask cmd=${2#wqflask/} - echo PYTHONPATH=$PYTHONPATH shift ; shift echo RUNNING COMMAND $cmd $* python $cmd $* @@ -151,7 +124,6 @@ fi if [ "$1" = "-cli" ] ; then cd $GN2_BASE_DIR/wqflask cmd=$2 - echo PYTHONPATH=$PYTHONPATH shift ; shift echo RUNNING COMMAND $cmd $* $cmd $* @@ -160,14 +132,12 @@ fi if [ "$1" = '-gunicorn' ] ; then cd $GN2_BASE_DIR/wqflask cmd=$2 - echo PYTHONPATH=$PYTHONPATH echo RUNNING gunicorn $cmd gunicorn $cmd exit $? fi if [ "$1" = '-gunicorn-dev' ] ; then cd $GN2_BASE_DIR/wqflask - echo PYTHONPATH=$PYTHONPATH if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi cmd="--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload wsgi" echo RUNNING gunicorn $cmd @@ -176,7 +146,6 @@ if [ "$1" = '-gunicorn-dev' ] ; then fi if [ "$1" = '-gunicorn-prod' ] ; then cd $GN2_BASE_DIR/wqflask - echo PYTHONPATH=$PYTHONPATH if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi PID=$TMPDIR/gunicorn.$USER.pid cmd="--bind 0.0.0.0:$SERVER_PORT --pid $PID --workers 20 --keep-alive 6000 --max-requests 100 --max-requests-jitter 30 --timeout 1200 wsgi" @@ -190,9 +159,6 @@ echo -n "dir $TMPDIR dbfilename gn2.rdb " | redis-server - & -# Overrides for packages that are not yet public (currently r-auwerx) -# export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib - # Start the flask server running GN2 cd $GN2_BASE_DIR/wqflask echo "Starting with $settings" |