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view build-and-run-job-scripts.sh @ 7:86f38533b2ab draft

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planemo upload for repository https://github.com/feltus/BDSS
author mingchen0919
date Tue, 12 Jun 2018 00:54:24 -0400
parents af2e4c66261f
children f7bd614bdb68
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# run job scripts within the tool outputs directory
cd ${REPORT_FILES_PATH}
mkdir download_dir

#========== build and run bdss-download.sh script ============
echo 'export PATH=/main/sites/galaxy/galaxy/tools/_conda/bin:$PATH' > bdss-download.sh
echo 'for u in $(echo $X_u | sed "s/,/ /g");' >> bdss-download.sh
echo 'do' >> bdss-download.sh
echo '  bdss transfer --destination download_dir -u $u' >> bdss-download.sh
echo 'done' >> bdss-download.sh
echo 'echo $(pwd)' >> bdss-download.sh

sh bdss-download.sh
# copy data from REPORT_FILES_PATHS to JOB_WORKING_DIR so that files can be discovered automatically.
cp -r download_dir ${JOB_WORKING_DIR}