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resources.sh
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resources.sh
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#!/bin/bash
SRC_DIR=$(dirname "$0")
function show_help {
echo "$0 - Create/Destroy resources for manual Cromwell workflow execution"
echo ""
echo "usage: sh $0 COMMAND --project <PROJECT> --bucket <BUCKET> --ip-range <RANGE>"
echo ""
echo "commands:"
echo " init-project Create required resources for the project. You'll almost always want this one."
echo " generate-config Generate the cromwell.conf file required by the VM"
echo " Use this when project init'd but no local copy"
echo ""
echo "arguments:"
echo " -h, --help print this block"
echo " --config-dir a dir path that is writable, DEFAULT='\$SRC_DIR'"
echo " --bucket name for the GCS bucket used by Cromwell"
echo " --project name of your GCP project"
echo " --ip-range block/range of acceptable IPs e.g. 172.16.0.0/24 or a single IP address e.g. 172.16.5.9/32 or a comma-seperated list of IPs/CIDRs."
echo " --gc-region DEFAULT='us-central1'. For other regions, check: https://cloud.google.com/compute/docs/regions-zones"
echo " --retention DEFAULT is none. For more option, check: https://cloud.google.com/storage/docs/gsutil/commands/mb#retention-policy"
echo ""
}
# die and opts based on this example
# http://mywiki.wooledge.org/BashFAQ/035
# --long-opt* example here
# https://stackoverflow.com/a/7069755
function die {
printf '%s\n' "$1" >&2 && exit 1
}
COMMAND=$1; shift
if [[ ($COMMAND != "init-project") && ($COMMAND != "generate-config")]]; then
show_help
die "ERROR: invalid command - $COMMAND"
fi
while test $# -gt 0; do
case $1 in
-h|--help)
show_help
exit
;;
--config-dir*)
if [ ! "$2" ]; then
CONFIG_DIR=$SRC_DIR
else
CONFIG_DIR=$2
shift
fi
;;
--bucket*)
if [ ! "$2" ]; then
die 'ERROR: "--bucket" requires a non-empty argument.'
else
BUCKET=$2
shift
fi
;;
--project*)
if [ ! "$2" ]; then
die 'ERROR: "--project" requires a non-empty argument.'
else
PROJECT=$2
shift
fi
;;
--ip-range*)
if [ ! "$2" ]; then
die 'ERROR: "--ip-range" requires a non-empty argument.'
else
IP_RANGE=$2
shift
fi
;;
--gc-region*)
if [ ! "$2" ]; then
GC_REGION="us-central1"
else
GC_REGION=$2
shift
fi
;;
--retention*)
if [ ! "$2" ]; then
RETENTION=""
else
RETENTION=$2
shift
fi
;;
*)
break
;;
esac
shift
done
if [ -z $CONFIG_DIR ]; then
CONFIG_DIR=$SRC_DIR
fi
if [ -z $PROJECT ]; then
die 'ERROR: "--project" must be set.'
fi
if [ -z $BUCKET ]; then
die 'ERROR: "--bucket" must be set.'
fi
if [ -z $IP_RANGE ]; then
die 'ERROR: "--ip-range" must be set.'
fi
if [ -z $GC_REGION ]; then
GC_REGION="us-central1"
fi
if [ -z $RETENTION ]; then
RETENTION=""
fi
COMPUTE_NAME="cromwell-compute"
SERVER_NAME="cromwell-server"
COMPUTE_ACCOUNT="$COMPUTE_NAME@$PROJECT.iam.gserviceaccount.com"
SERVER_ACCOUNT="$SERVER_NAME@$PROJECT.iam.gserviceaccount.com"
function generate_config {
cp $SRC_DIR/base_cromwell.conf $CONFIG_DIR/cromwell.conf
cat << EOF >> $CONFIG_DIR/cromwell.conf
backend.providers.default.config {
project = "$PROJECT"
root = "gs://$BUCKET/cromwell-executions"
genomics.compute-service-account = "$COMPUTE_ACCOUNT"
filesystems.gcs.project = "$PROJECT"
}
EOF
cat <<EOF > $CONFIG_DIR/workflow_options.json
{
"default_runtime_attributes": {
"preemptible": 1,
"maxRetries": 2
},
"final_workflow_log_dir": "gs://$BUCKET/final-logs",
"final_call_logs": "gs://$BUCKET/call-logs"
}
EOF
}
sh $SRC_DIR/../scripts/enable_api.sh
case $COMMAND in
"init-project")
# Create service accounts
sh $SRC_DIR/../scripts/create_resources.sh $PROJECT $SERVER_NAME $COMPUTE_NAME $BUCKET $IP_RANGE $GC_REGION $RETENTION
# Create bucket if not exists
# Generate cromwell.conf
generate_config
;;
"generate-config")
generate_config
;;
esac
cat <<EOF
Completed $COMMAND. Check stderr logs and make sure nothing unexpected
happened. Script optimistically executes and will relay gcloud's error on
redundant operations, e.g. creating a resource that already exists.
Service Account: $SERVER_ACCOUNT
EOF