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-rwxr-xr-xbin/genenetwork2104
1 files changed, 58 insertions, 46 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 52d3155c..df688989 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=$GN2_PROFILE/site-library
+ export GUIX_JS_PATH=$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 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