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Improve startup scripts
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Fix errors reported by shellcheck
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@nsoranzo
nsoranzo committed Aug 11, 2016
1 parent e5e2996 commit 87d6239
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Showing 2 changed files with 30 additions and 30 deletions.
22 changes: 11 additions & 11 deletions run.sh
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#!/bin/sh

cd `dirname $0`
cd "$(dirname "$0")"

# If there is a file that defines a shell environment specific to this
# instance of Galaxy, source the file.
Expand Down Expand Up @@ -34,7 +34,7 @@ do
shift
;;
--daemon|--restart|restart)
if [ "$1"=="--restart" ]
if [ "$1" = "--restart" ]
then
paster_args="$paster_args restart"
else
Expand Down Expand Up @@ -66,7 +66,7 @@ GALAXY_VIRTUAL_ENV="${GALAXY_VIRTUAL_ENV:-.venv}"
if [ -d "$GALAXY_VIRTUAL_ENV" -a -z "$skip_venv" ];
then
[ -n "$PYTHONPATH" ] && { echo 'Unsetting $PYTHONPATH'; unset PYTHONPATH; }
printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
echo "Activating virtualenv at $GALAXY_VIRTUAL_ENV"
. "$GALAXY_VIRTUAL_ENV/bin/activate"
fi

Expand Down Expand Up @@ -99,35 +99,35 @@ if [ -z "$GALAXY_CONFIG_FILE" ]; then
fi

if [ -n "$GALAXY_RUN_ALL" ]; then
servers=`sed -n 's/^\[server:\(.*\)\]/\1/ p' $GALAXY_CONFIG_FILE | xargs echo`
servers=$(sed -n 's/^\[server:\(.*\)\]/\1/ p' "$GALAXY_CONFIG_FILE" | xargs echo)
if [ -z "$stop_daemon_arg_set" -a -z "$daemon_or_restart_arg_set" ]; then
echo 'ERROR: $GALAXY_RUN_ALL cannot be used without the `--daemon`, `--stop-daemon` or `restart` arguments to run.sh'
echo "ERROR: \$GALAXY_RUN_ALL cannot be used without the '--daemon', '--stop-daemon' or 'restart' arguments to run.sh"
exit 1
fi
for server in $servers; do
if [ -n "$wait_arg_set" -a -n "$daemon_or_restart_arg_set" ]; then
python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $paster_args
python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" --server-name="$server" --pid-file="$server.pid" --log-file="$server.log" $paster_args
while true; do
sleep 1
printf "."
# Grab the current pid from the pid file
if ! current_pid_in_file=$(cat $server.pid); then
if ! current_pid_in_file=$(cat "$server.pid"); then
echo "A Galaxy process died, interrupting" >&2
exit 1
fi
# Search for all pids in the logs and tail for the last one
latest_pid=`egrep '^Starting server in PID [0-9]+\.$' $server.log -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1`
latest_pid=$(egrep '^Starting server in PID [0-9]+\.$' "$server.log" -o | sed 's/Starting server in PID //g;s/\.$//g' | tail -n 1)
# If they're equivalent, then the current pid file agrees with our logs
# and we've succesfully started
[ -n "$latest_pid" ] && [ $latest_pid -eq $current_pid_in_file ] && break
[ -n "$latest_pid" ] && [ "$latest_pid" -eq "$current_pid_in_file" ] && break
done
echo
else
echo "Handling $server with log file $server.log..."
python ./scripts/paster.py serve $GALAXY_CONFIG_FILE --server-name=$server --pid-file=$server.pid --log-file=$server.log $paster_args
python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" --server-name="$server" --pid-file="$server.pid" --log-file="$server.log" $paster_args
fi
done
else
# Handle only 1 server, whose name can be specified with --server-name parameter (defaults to "main")
python ./scripts/paster.py serve $GALAXY_CONFIG_FILE $paster_args
python ./scripts/paster.py serve "$GALAXY_CONFIG_FILE" $paster_args
fi
38 changes: 19 additions & 19 deletions scripts/common_startup.sh
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
#!/bin/bash
#!/bin/sh
set -e

SET_VENV=1
Expand Down Expand Up @@ -54,22 +54,22 @@ if [ $COPY_SAMPLE_FILES -eq 1 ]; then
for sample in $SAMPLES; do
file=${sample%.sample}
if [ ! -f "$file" -a -f "$sample" ]; then
echo "Initializing $file from `basename $sample`"
cp $sample $file
echo "Initializing $file from $(basename "$sample")"
cp "$sample" "$file"
fi
done
fi

# remove problematic cached files
for rmfile in $RMFILES; do
[ -f $rmfile ] && rm -f $rmfile
[ -f "$rmfile" ] && rm -f "$rmfile"
done

: ${GALAXY_CONFIG_FILE:=config/galaxy.ini}
if [ ! -f $GALAXY_CONFIG_FILE ]; then
if [ ! -f "$GALAXY_CONFIG_FILE" ]; then
GALAXY_CONFIG_FILE=universe_wsgi.ini
fi
if [ ! -f $GALAXY_CONFIG_FILE ]; then
if [ ! -f "$GALAXY_CONFIG_FILE" ]; then
GALAXY_CONFIG_FILE=config/galaxy.ini.sample
fi

Expand All @@ -87,24 +87,24 @@ if [ $SET_VENV -eq 1 -a $CREATE_VENV -eq 1 ]; then
vvers=13.1.2
vurl="https://pypi.python.org/packages/source/v/virtualenv/virtualenv-${vvers}.tar.gz"
vsha="aabc8ef18cddbd8a2a9c7f92bc43e2fea54b1147330d65db920ef3ce9812e3dc"
vtmp=`mktemp -d -t galaxy-virtualenv-XXXXXX`
vsrc="$vtmp/`basename $vurl`"
vtmp=$(mktemp -d -t galaxy-virtualenv-XXXXXX)
vsrc="$vtmp/$(basename $vurl)"
# SSL certificates are not checked to prevent problems with messed
# up client cert environments. We verify the download using a known
# good sha256 sum instead.
echo "Fetching $vurl"
if command -v curl >/dev/null; then
curl --insecure -L -o $vsrc $vurl
curl --insecure -L -o "$vsrc" "$vurl"
elif command -v wget >/dev/null; then
wget --no-check-certificate -O $vsrc $vurl
wget --no-check-certificate -O "$vsrc" "$vurl"
else
python -c "import urllib; urllib.urlretrieve('$vurl', '$vsrc')"
fi
echo "Verifying $vsrc checksum is $vsha"
python -c "import hashlib; assert hashlib.sha256(open('$vsrc', 'rb').read()).hexdigest() == '$vsha', '$vsrc: invalid checksum'"
tar zxf $vsrc -C $vtmp
python $vtmp/virtualenv-$vvers/virtualenv.py "$GALAXY_VIRTUAL_ENV"
rm -rf $vtmp
tar zxf "$vsrc" -C "$vtmp"
python "$vtmp/virtualenv-$vvers/virtualenv.py" "$GALAXY_VIRTUAL_ENV"
rm -rf "$vtmp"
fi
fi
fi
Expand All @@ -114,7 +114,7 @@ if [ $SET_VENV -eq 1 ]; then
# should run this instance in.
if [ -d "$GALAXY_VIRTUAL_ENV" ];
then
printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
echo "Activating virtualenv at $GALAXY_VIRTUAL_ENV"
. "$GALAXY_VIRTUAL_ENV/bin/activate"
# Because it's a virtualenv, we assume $PYTHONPATH is unnecessary for
# anything in the venv to work correctly, and having it set can cause
Expand All @@ -131,7 +131,7 @@ if [ $SET_VENV -eq 1 ]; then
exit 1
fi
elif [ $SET_VENV -eq 0 -a $CONDA_ALREADY_INSTALLED -eq 1 ]; then
echo -e "\e[33mWarning: You have Conda installed. Skipping virtualenv activation. This could cause missing dependencies.\e[0m"
echo "Warning: You have Conda installed. Skipping virtualenv activation. This could cause missing dependencies."
fi

: ${GALAXY_WHEELS_INDEX_URL:="https://wheels.galaxyproject.org/simple"}
Expand All @@ -140,12 +140,12 @@ if [ $REPLACE_PIP -eq 1 ]; then
fi

if [ $FETCH_WHEELS -eq 1 ]; then
pip install -r requirements.txt --index-url ${GALAXY_WHEELS_INDEX_URL}
GALAXY_CONDITIONAL_DEPENDENCIES=`PYTHONPATH=lib python -c "import galaxy.dependencies; print '\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE'))"`
[ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url ${GALAXY_WHEELS_INDEX_URL}
pip install -r requirements.txt --index-url "${GALAXY_WHEELS_INDEX_URL}"
GALAXY_CONDITIONAL_DEPENDENCIES=$(PYTHONPATH=lib python -c "import galaxy.dependencies; print '\n'.join(galaxy.dependencies.optional('$GALAXY_CONFIG_FILE'))")
[ -z "$GALAXY_CONDITIONAL_DEPENDENCIES" ] || echo "$GALAXY_CONDITIONAL_DEPENDENCIES" | pip install -r /dev/stdin --index-url "${GALAXY_WHEELS_INDEX_URL}"
fi

if [ $FETCH_WHEELS -eq 1 -a $DEV_WHEELS -eq 1 ]; then
dev_requirements='./lib/galaxy/dependencies/dev-requirements.txt'
[ -f $dev_requirements ] && pip install -r $dev_requirements --index-url ${GALAXY_WHEELS_INDEX_URL}
[ -f $dev_requirements ] && pip install -r $dev_requirements --index-url "${GALAXY_WHEELS_INDEX_URL}"
fi

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