[9271c5]: / source / GenomicsAnalysisCode / run_crawlers.sh

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#!/bin/bash -e
export AWS_DEFAULT_OUTPUT=text
project_name=$1
# start imaging crawlers
imaging_crawlers=$(
aws cloudformation describe-stack-resources \
--stack-name "${project_name}-Imaging" \
--query 'StackResources[?ResourceType==`AWS::Glue::Crawler`].PhysicalResourceId')
for img_crawler_name in ${imaging_crawlers}; do
aws glue start-crawler --name ${img_crawler_name}
done
printf "Crawlers started successfully\n"
# start glue jobs (not needed)
#workflow_name=$(aws cloudformation describe-stacks \
# --stack-name "${project_name}-Imaging" \
# --query 'Stacks[0].Outputs[?OutputKey==`TCGAWorkflow`].OutputValue')
#
#aws glue start-workflow-run --name ${workflow_name}