diff options
Diffstat (limited to 'bin')
| -rwxr-xr-x | bin/genenetwork2 | 164 |
1 files changed, 114 insertions, 50 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index ce3678e4..36bf11a6 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -1,67 +1,79 @@ -#! /bin/sh -e +#! /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 # -# ./bin/genenetwork2 ~/my_settings.py +# 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). +# supplied). Typically you need a GNU Guix profile which is set with +# an environment variable (this profile is dictated by the +# installation path of genenetwork). Say your profile is in +# ~/opt/gn-latest-guix +# +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 +# +# You can pass in your own settings file, e.g. +# +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ~/my_settings.py # # To run a maintenance python script with settings (instead of the # webserver) run from the base-dir with settings file and add that # script with a -c switch, e.g. # -# env TMPDIR=/export/local/home/zas1024/gn2-zach/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5002 GENENETWORK_FILES=/export/local/home/zas1024/gn2-zach/genotype_files SQL_URI=mysql://webqtlout:webqtlout@lily.uthsc.edu/db_webqtl ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_select_dataset.py +# env GN2_PROFILE=/usr/local/guix-profiles/gn-latest-20190905 TMPDIR=/export/local/home/zas1024/gn2-zach/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5002 GENENETWORK_FILES=/export/local/home/zas1024/gn2-zach/genotype_files SQL_URI=mysql://webqtlout:webqtlout@lily.uthsc.edu/db_webqtl ./bin/genenetwork2 ./etc/default_settings.py -c ./maintenance/gen_select_dataset.py # # To run any script in the environment # -# ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD" +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD" # # To get a python REPL(!) # -# ./bin/genenetwork2 ./etc/default_settings.py -cli python +# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli python # # For development you may want to run # -# env WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2 +# env GN2_PROFILE=~/opt/gn-latest 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 SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-prod +# env GN2_PROFILE=~/opt/gn-latest-guix SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-prod # # For development use # -# env SERVER_PORT=5003 ./bin/genenetwork2 ./etc/default_settings.py -gunicorn-dev +# 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 # -# ./bin/genenetwork2 ./etc/default_settings.py -gunicorn "--bind 0.0.0.0:5003 --workers=1 wsgi" +# 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 -export GN2_PROFILE=$GUIX_ENVIRONMENT -echo GN2_PROFILE=$GN2_PROFILE -GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT")) -GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR) +echo SCRIPT="${SCRIPT}" +echo GN2_PROFILE="${GN2_PROFILE}" +GN2_BASE_DIR=$(dirname "$(dirname "${SCRIPT}")") +GN2_ID=$(cat /etc/hostname):$(basename "${GN2_BASE_DIR}") -echo GN2_BASE_DIR=$GN2_BASE_DIR +echo GN2_BASE_DIR="${GN2_BASE_DIR}" GUIX_SITE=$GN2_BASE_DIR/lib/python3.8/site-packages -if [ -d $GUIX_SITE ]; then +if [ -d "${GUIX_SITE}" ]; then echo INFO: GN2 is running from GNU Guix GN2_BASE_DIR=$GUIX_SITE - export GN_VERSION=$GN2_ID:$(cat $GN2_BASE_DIR/etc/VERSION) + GN_VERSION="${GN2_ID}:$(cat "${GN2_BASE_DIR}"/etc/VERSION)" + export GN_VERSION else echo INFO: GN2 is running from a source tree GIT_HASH=$(git rev-parse HEAD) GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD) - export GN_VERSION=$GN2_ID:$(cat $GN2_BASE_DIR/etc/VERSION)-$GIT_BRANCH-${GIT_HASH:0:9} + GN_VERSION="${GN2_ID}:$(cat "${GN2_BASE_DIR}"/etc/VERSION)-${GIT_BRANCH}-$(echo "${GIT_HASH}" | cut -c1-9)" + export GN_VERSION fi -echo GN_VERSION=$GN_VERSION +echo GN_VERSION="${GN_VERSION}" if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then echo "Can not use $1 switch without default settings file" @@ -69,12 +81,12 @@ if [ "$1" = "-c" -o "$1" = "-gunicorn" ]; then fi settings=$1 -if [ -z $settings ]; then +if [ -z "${settings}" ]; then settings=$GN2_BASE_DIR/etc/default_settings.py else shift fi -settings=$(realpath $settings) +settings=$(realpath "${settings}") # ext="${settings##*.}" # if [ "$ext" = "json" -o "$ext" = "JSON" ]; then @@ -83,83 +95,135 @@ settings=$(realpath $settings) # echo $settings # fi -if [ ! -e $settings ]; then +if [ ! -e "${settings}" ]; then echo "ERROR: can not locate settings file - pass it in the command line" exit 1 fi export GN2_SETTINGS=$settings # Python -echo GN2_SETTINGS=$settings - -export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript -export LC_ALL=C # FIXME -export GUIX_GENENETWORK_FILES="$GN2_PROFILE/share/genenetwork2" -export PLINK_COMMAND="$GN2_PROFILE/bin/plink2" -export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma" -if [ -z $GEMMA_WRAPPER_COMMAND ]; then - export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper" +echo GN2_SETTINGS="${settings}" + +if [ -z "${GN2_PROFILE}" ] ; then + echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!" + GN2_PROFILE=$(dirname $(dirname $(which genenetwork2))) + export GN2_PROFILE + if [ -d "${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..." +else + export PATH=$GN2_PROFILE/bin:$PATH + export PYTHONPATH="$GN2_PROFILE/lib/python3.9/site-packages" # never inject another PYTHONPATH!! + export R_LIBS_SITE=$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="$GN2_PROFILE/bin/plink2" + export GEMMA_COMMAND="$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 ${R_LIBS_SITE}" ; exit 1 ; fi +fi +if [ -z "${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:$PYTHONPATH + +export PYTHONPATH="${GN3_DEV_REPO_PATH:+$GN3_DEV_REPO_PATH:}:${PYTHONPATH}" + # Our UNIX TMPDIR defaults to /tmp - change this on a shared server -if [ -z $TMPDIR ]; then +if [ -z "${TMPDIR}" ]; then TMPDIR="/tmp" fi # Show environment settings set|grep guix -set|grep $GN2_PROFILE +set|grep GN2_PROFILE set|grep TMPDIR # Now handle command parameter -c which runs python if [ "$1" = '-c' ] ; then - cd $GN2_BASE_DIR/wqflask + cd "${GN2_BASE_DIR}/wqflask" cmd=${2#wqflask/} + echo PYTHONPATH="${PYTHONPATH}" shift ; shift - echo RUNNING COMMAND $cmd $* + echo "RUNNING COMMAND ${cmd} ${*}" python $cmd $* exit $? fi # Now handle command parameter -cli which runs in bash if [ "$1" = "-cli" ] ; then - cd $GN2_BASE_DIR/wqflask + cd "${GN2_BASE_DIR}/wqflask" cmd=$2 + echo PYTHONPATH="${PYTHONPATH}" shift ; shift - echo RUNNING COMMAND $cmd $* + echo "RUNNING COMMAND ${cmd} ${*}" $cmd $* exit $? fi if [ "$1" = '-gunicorn' ] ; then - cd $GN2_BASE_DIR/wqflask + cd "${GN2_BASE_DIR}/wqflask" cmd=$2 - echo RUNNING gunicorn $cmd + echo PYTHONPATH="${PYTHONPATH}" + echo "RUNNING gunicorn ${cmd}" gunicorn $cmd exit $? fi if [ "$1" = '-gunicorn-dev' ] ; then - cd $GN2_BASE_DIR/wqflask - 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 $cmd + cd "${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 run_gunicorn:app" + echo "RUNNING gunicorn ${cmd}" gunicorn $cmd exit $? fi if [ "$1" = '-gunicorn-prod' ] ; then - cd $GN2_BASE_DIR/wqflask - if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi + cd "${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" - echo RUNNING gunicorn $cmd + echo "RUNNING gunicorn ${cmd}" gunicorn $cmd exit $? fi -echo "Starting the redis server:" -echo -n "dir $TMPDIR +if [ -z "$NO_REDIS" ] ; then + echo "Starting the redis server:" + echo -n "dir $TMPDIR dbfilename gn2.rdb " | redis-server - & +fi + +# Overrides for packages that are not yet public (currently r-auwerx) +# export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib # Start the flask server running GN2 -cd $GN2_BASE_DIR/wqflask +cd "${GN2_BASE_DIR}/wqflask" echo "Starting with $settings" python runserver.py |