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authorArun Isaac2022-01-03 17:51:04 +0530
committerArun Isaac2022-01-06 10:01:05 +0530
commit344e428126b60932bff4c62c5ded8c36519155e8 (patch)
treefd89b7242809826c608dab6b6645380e8e818100 /bin
parentf4e336eb1ea526156e112cff97a3ec8137a2bc90 (diff)
downloadgenenetwork2-344e428126b60932bff4c62c5ded8c36519155e8.tar.gz
bin: Do not set environment variables set by guix shell.
The Guix python package accepts GUIX_PYTHONPATH instead of PYTHONPATH. `guix shell' sets GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, GUIX_PYTHONPATH, PATH, R_LIB_SITE and XDG_DATA_DIRS when necessary. There is no need to set these environment variables explicitly. * bin/genenetwork2: Do not set GI_TYPELIB_PATH, GIO_EXTRA_MODULES, GUIX_GTK3_PATH, PATH, PYTHONPATH, R_LIBS_SITE and XDG_DATA_DIRS. * README.md [Development]: Remove paragraph on injecting python modules locally.
Diffstat (limited to 'bin')
-rwxr-xr-xbin/genenetwork234
1 files changed, 0 insertions, 34 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 93ab02f8..934a10d8 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -91,14 +91,7 @@ fi
export GN2_SETTINGS=$settings # Python
echo GN2_SETTINGS=$settings
-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="$GN2_PROFILE/bin/plink2"
@@ -106,25 +99,6 @@ export GEMMA_COMMAND="$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
-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
# Our UNIX TMPDIR defaults to /tmp - change this on a shared server
if [ -z $TMPDIR ]; then
@@ -140,7 +114,6 @@ set|grep TMPDIR
if [ "$1" = '-c' ] ; then
cd $GN2_BASE_DIR/wqflask
cmd=${2#wqflask/}
- echo PYTHONPATH=$PYTHONPATH
shift ; shift
echo RUNNING COMMAND $cmd $*
python $cmd $*
@@ -151,7 +124,6 @@ fi
if [ "$1" = "-cli" ] ; then
cd $GN2_BASE_DIR/wqflask
cmd=$2
- echo PYTHONPATH=$PYTHONPATH
shift ; shift
echo RUNNING COMMAND $cmd $*
$cmd $*
@@ -160,14 +132,12 @@ fi
if [ "$1" = '-gunicorn' ] ; then
cd $GN2_BASE_DIR/wqflask
cmd=$2
- echo PYTHONPATH=$PYTHONPATH
echo RUNNING gunicorn $cmd
gunicorn $cmd
exit $?
fi
if [ "$1" = '-gunicorn-dev' ] ; 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=1 --timeout 180 --reload wsgi"
echo RUNNING gunicorn $cmd
@@ -176,7 +146,6 @@ if [ "$1" = '-gunicorn-dev' ] ; then
fi
if [ "$1" = '-gunicorn-prod' ] ; then
cd $GN2_BASE_DIR/wqflask
- echo PYTHONPATH=$PYTHONPATH
if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi
PID=$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"
@@ -190,9 +159,6 @@ echo -n "dir $TMPDIR
dbfilename gn2.rdb
" | redis-server - &
-# Overrides for packages that are not yet public (currently r-auwerx)
-# export R_LIBS_SITE=$R_LIBS_SITE:$HOME/.Rlibs/das1i1pm54dj6lbdcsw5w0sdwhccyj1a-r-3.3.2/lib/R/lib
-
# Start the flask server running GN2
cd $GN2_BASE_DIR/wqflask
echo "Starting with $settings"