diff options
Diffstat (limited to 'bin/genenetwork2')
| -rwxr-xr-x | bin/genenetwork2 | 104 |
1 files changed, 58 insertions, 46 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 52d3155c..236d8f63 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -1,34 +1,39 @@ #! /bin/bash # # This will run the GN2 server (with default settings if none -# supplied). Pass in your own settings file, e.g. +# 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 # -# ./bin/genenetwork2 ~/my_settings.py +# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 # -# But better is to retain the defaults and override them with -# JSON file (see the deploy docs). +# You can pass in your own settings file, e.g. # -# ./bin/genenetwork2 ~/my_overrides.json +# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_settings.py # # To run a maintenance script with settings (instead of the webserver) add that with # a -c switch, e.g. # -# ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py -# -# Environment settings can be used to preconfigure as well as a -# settings.py file. -# -# GN2_BASE_PATH is base directory of wqflask source code -# +# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py SCRIPT=$(readlink -f "$0") GN2_BASE_DIR=$(dirname $(dirname "$SCRIPT")) +GN2_ID=$(cat /etc/hostname):$(basename $GN2_BASE_DIR) echo GN2_BASE_DIR=$GN2_BASE_DIR -GIT_HASH=$(git rev-parse HEAD) -GIT_BRANCH=$(git rev-parse --abbrev-ref HEAD) -export GN_VERSION=$(cat $GN2_BASE_DIR/VERSION)-$GIT_BRANCH-${GIT_HASH:0:9} +GUIX_SITE=$GN2_BASE_DIR/lib/python2.7/site-packages +if [ -d $GUIX_SITE ]; then + echo INFO: GN2 is running from GNU Guix + GN2_BASE_DIR=$GUIX_SITE + export GN_VERSION=$GN2_ID:$(cat $GN2_BASE_DIR/etc/VERSION) +else + echo INFO: GN2 is running from a source tree + GIT_HASH=$(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-${GIT_HASH:0:9} +fi echo GN_VERSION=$GN_VERSION # Handle settings parameter (can be .py or .json) @@ -41,13 +46,8 @@ else shift fi if [ ! -e $settings ]; then - GUIX_ETC=$GN2_BASE_DIR/lib/python2.7/site-packages/genenetwork2-2.0-py2.7.egg - if [ -d $GUIX_ETC ]; then - echo INFO: GN2 is actually running from GNU Guix - else - echo "ERROR: can not locate settings file - pass it in the command line" - exit 1 - fi + echo "ERROR: can not locate settings file - pass it in the command line" + exit 1 fi export WQFLASK_SETTINGS=$settings # Python export WQFLASK_OVERRIDES=$overrides # JSON @@ -55,30 +55,40 @@ export WQFLASK_OVERRIDES=$overrides # JSON echo WQFLASK_SETTINGS=$settings echo WQFLASK_OVERRIDES=$overrides -# ---- Checks and balances -if [ -z $GUIX_ETC ]; then - if [ -z $GN2_PROFILE ] ; then - echo "WARNING: GN2_PROFILE has not been set - I hope you know what you are doing!" - else - export PATH=$GN2_PROFILE/bin:$PATH - export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages - export R_LIBS_SITE=$GN2_PROFILE/site-library - export GUIX_GTK3_PATH="$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 - fi - if [ -z $PYTHONPATH ] ; then - echo "WARNING PYTHONPATH has not been set - use GN2_PROFILE!" - 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 +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 fi +if [ -z $GN2_PROFILE ]; then + read -p "PRESS [ENTER] TO CONTINUE..." +else + export PATH=$GN2_PROFILE/bin:$PATH + export PYTHONPATH=$GN2_PROFILE/lib/python2.7/site-packages + 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 PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis" + export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma" +fi +if [ -z $PYTHONPATH ] ; then + echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!" + exit 1 +fi +if [ ! -d $R_LIBS_SITE ] ; then + echo "ERROR R_LIBS_SITE has not been set correctly (we only allow one path) - use GN2_PROFILE!" + echo "Paste into your shell the output of (for example)" + echo "guix package -p \$GN2_PROFILE --search-paths" + exit 1 +fi # We may change this one: export PYTHONPATH=$GN2_BASE_DIR/wqflask:$PYTHONPATH @@ -88,6 +98,8 @@ if [ -z $TMPDIR ]; then TMPDIR="/tmp" fi +# Show environment settings +set|grep guix set|grep $GN2_PROFILE set|grep TMPDIR @@ -97,7 +109,7 @@ if [ "$1" = '-c' ] ; then cmd=${2#wqflask/} echo PYTHONPATH=$PYTHONPATH echo RUNNING COMMAND $cmd - /usr/bin/env python $cmd + python $cmd exit 0 fi @@ -109,4 +121,4 @@ dbfilename gn2.rdb # Start the flask server running GN2 cd $GN2_BASE_DIR/wqflask echo "Starting with $settings" -/usr/bin/env python runserver.py +python runserver.py |