diff options
Diffstat (limited to 'bin/genenetwork2')
| -rwxr-xr-x | bin/genenetwork2 | 30 |
1 files changed, 25 insertions, 5 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index cbaba76f..8886e4bc 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -1,8 +1,11 @@ #! /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 +# env GN2_PROFILE=~/opt/genenetwork2-phewas ./bin/genenetwork2 ~/my_settings.py # # Where GN2_PROFILE points to the GNU Guix profile used for deployment. # @@ -41,6 +44,8 @@ # env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -gunicorn "--bind 0.0.0.0:5003 --workers=1 wsgi" 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) @@ -96,6 +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 $GN2_PROFILE ]; then read -p "PRESS [ENTER] TO CONTINUE..." @@ -114,7 +121,9 @@ else export PLINK_COMMAND="$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 @@ -143,7 +152,7 @@ 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/} @@ -152,6 +161,16 @@ 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 + echo RUNNING COMMAND $cmd + $cmd + exit $? +fi if [ "$1" = '-gunicorn' ] ; then cd $GN2_BASE_DIR/wqflask cmd=$2 @@ -164,7 +183,7 @@ 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 --reload wsgi" + cmd="--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload wsgi" echo RUNNING gunicorn $cmd gunicorn $cmd exit $? @@ -173,7 +192,8 @@ if [ "$1" = '-gunicorn-prod' ] ; then cd $GN2_BASE_DIR/wqflask echo PYTHONPATH=$PYTHONPATH if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi - cmd="--bind 0.0.0.0:$SERVER_PORT --workers=32 --max-requests 1000 --timeout 1200 wsgi" + 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 $? |