diff options
Diffstat (limited to 'bin/genenetwork2')
| -rwxr-xr-x | bin/genenetwork2 | 83 |
1 files changed, 30 insertions, 53 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index b5c940a8..93ab02f8 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -5,55 +5,45 @@ # # 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. +# ./bin/genenetwork2 ~/my_settings.py # # 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 -# 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 +# supplied). # # 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 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 +# 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 # # To run any script in the environment # -# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD" +# ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD" # # To get a python REPL(!) # -# env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -cli python +# ./bin/genenetwork2 ./etc/default_settings.py -cli python # # For development you may want to run # -# env GN2_PROFILE=~/opt/gn-latest WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG ./bin/genenetwork2 +# env 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 +# env 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 +# env 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" +# ./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 $GN2_BASE_DIR) @@ -101,40 +91,27 @@ fi export GN2_SETTINGS=$settings # Python echo GN2_SETTINGS=$settings -if [ -z $GN2_PROFILE ] ; then - echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!" - export GN2_PROFILE=$(dirname $(dirname $(which genenetwork2))) - 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/python3.8/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" - 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 +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="$GN2_PROFILE/bin/plink2" +export GEMMA_COMMAND="$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 |