diff options
| -rw-r--r-- | README.md | 4 | ||||
| -rwxr-xr-x | bin/genenetwork2 | 34 |
2 files changed, 38 insertions, 0 deletions
@@ -46,6 +46,10 @@ 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 7669a89a..f1e04eef 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -91,7 +91,14 @@ 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="$GN2_PROFILE/bin/plink2" @@ -99,6 +106,25 @@ export GEMMA_COMMAND="$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 @@ -114,6 +140,7 @@ 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 $* @@ -124,6 +151,7 @@ fi if [ "$1" = "-cli" ] ; then cd $GN2_BASE_DIR/wqflask cmd=$2 + echo PYTHONPATH=$PYTHONPATH shift ; shift echo RUNNING COMMAND $cmd $* $cmd $* @@ -132,12 +160,14 @@ 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 @@ -146,6 +176,7 @@ 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" @@ -159,6 +190,9 @@ 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" |