diff options
Diffstat (limited to 'bin/genenetwork2')
| -rwxr-xr-x | bin/genenetwork2 | 103 |
1 files changed, 95 insertions, 8 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 5e791885..8886e4bc 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -1,5 +1,14 @@ #! /bin/bash # +# This is the startup script for GN2. It sets the environment variables to pick +# up a Guix profile and allows for overriding parameters. +# +# Typical usage +# +# env GN2_PROFILE=~/opt/genenetwork2-phewas ./bin/genenetwork2 ~/my_settings.py +# +# Where GN2_PROFILE points to the GNU Guix profile used for deployment. +# # This will run the GN2 server (with default settings if none # supplied). Typically you need a GNU Guix profile which is set with # an environment variable (this profile is dictated by the @@ -16,8 +25,27 @@ # a -c switch, e.g. # # env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py +# +# For development you may want to run +# +# env GN2_PROFILE=~/opt/gn-latest-guix WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2 +# +# For staging and production we use gunicorn. Run with something like +# (note you have to provide the server port). Provide a settings file! +# +# env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-prod +# +# For development use +# +# env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev +# +# For extra flexibility you can also provide gunicorn parameters yourself with something like +# +# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -gunicorn "--bind 0.0.0.0:5003 --workers=1 wsgi" -SCRIPT=$(readlink -f "$0") +SCRIPT=$(realpath "$0") +echo SCRIPT=$SCRIPT +echo GN2_PROFILE=$GN2_PROFILE GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT")) GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR) @@ -36,15 +64,27 @@ else fi echo GN_VERSION=$GN_VERSION +if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then + echo "Can not use $1 switch without default settings file" + exit 1 +fi # Handle settings parameter (can be .py or .json) -settings=$1 +if [ ! -z $1 ]; then + settings=$(realpath "$1") + if [ ! -e $settings ]; then + settings=$GN2_BASE_DIR/etc/default_settings.py + else + shift + fi +fi + ext="${settings##*.}" -if [ -z "$settings" -o "$ext" = "json" -o "$ext" = "JSON" ]; then +if [ "$ext" = "json" -o "$ext" = "JSON" ]; then overrides=$settings - settings=$GN2_BASE_DIR/etc/default_settings.py else - shift + echo $settings fi + if [ ! -e $settings ]; then echo "ERROR: can not locate settings file - pass it in the command line" exit 1 @@ -61,6 +101,8 @@ if [ -z $GN2_PROFILE ] ; then if [ -d $GN2_PROFILE ]; then echo "Best guess is $GN2_PROFILE" fi + echo "ERROR: always set GN2_PROFILE" + exit 1 fi if [ -z $GN2_PROFILE ]; then read -p "PRESS [ENTER] TO CONTINUE..." @@ -79,7 +121,12 @@ else export PLINK_COMMAND="$GN2_PROFILE/bin/plink2" export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis" export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma" - export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper" + if [ -z $GEMMA_WRAPPER_COMMAND ]; then + export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper" + fi + if [ ! -d $PYTHONPATH ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi + 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!" @@ -105,14 +152,51 @@ set|grep guix set|grep $GN2_PROFILE set|grep TMPDIR -# Now handle command parameter -c +# Now handle command parameter -c which runs python if [ "$1" = '-c' ] ; then cd $GN2_BASE_DIR/wqflask cmd=${2#wqflask/} echo PYTHONPATH=$PYTHONPATH echo RUNNING COMMAND $cmd python $cmd - exit 0 + 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 + echo RUNNING COMMAND $cmd + $cmd + exit $? +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 + gunicorn $cmd + exit $? +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 -k eventlet --workers 20 --keep-alive 1200 --max-requests 1000 --timeout 1200 wsgi" + echo RUNNING gunicorn $cmd + gunicorn $cmd + exit $? fi echo "Starting the redis server:" @@ -120,6 +204,9 @@ 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" |