diff options
Diffstat (limited to 'bin/genenetwork2')
| -rwxr-xr-x | bin/genenetwork2 | 30 |
1 files changed, 19 insertions, 11 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 145ce395..2a83a1cd 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -45,6 +45,7 @@ SCRIPT=$(realpath "$0") echo SCRIPT=$SCRIPT +echo GN2_PROFILE=$GN2_PROFILE GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT")) GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR) @@ -94,11 +95,13 @@ export WQFLASK_OVERRIDES=$overrides # JSON echo WQFLASK_SETTINGS=$settings echo WQFLASK_OVERRIDES=$overrides -if [ -z $ELASTICSEARCH_PROFILE ]; then - echo -e "\033[1;33mWARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE\033[0m"; -else - PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages" -fi +# This is a temporary hack to inject ES - should have added python2-elasticsearch package to guix instead +# if [ -z $ELASTICSEARCH_PROFILE ]; then +# echo -e "WARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE"; +# else +# PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages" +# fi + if [ -z $GN2_PROFILE ] ; then echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!" export GN2_PROFILE=$(dirname $(dirname $(which genenetwork2))) @@ -125,7 +128,9 @@ else export PLINK_COMMAND="$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 while IFS=":" read -ra PPATH; do for PPart in "${PPATH[@]}"; do if [ ! -d $PPart ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi @@ -163,8 +168,9 @@ if [ "$1" = '-c' ] ; then cd $GN2_BASE_DIR/wqflask cmd=${2#wqflask/} echo PYTHONPATH=$PYTHONPATH - echo RUNNING COMMAND $cmd - python $cmd + shift ; shift + echo RUNNING COMMAND $cmd $* + python $cmd $* exit $? fi # Now handle command parameter -cli which runs in bash @@ -173,8 +179,9 @@ if [ "$1" = "-cli" ] ; then cd $GN2_BASE_DIR/wqflask cmd=$2 echo PYTHONPATH=$PYTHONPATH - echo RUNNING COMMAND $cmd - $cmd + shift ; shift + echo RUNNING COMMAND $cmd $* + $cmd $* exit $? fi if [ "$1" = '-gunicorn' ] ; then @@ -198,7 +205,8 @@ 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 $? |