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annotate build-and-run-job-scripts.sh @ 1:a110308993be draft

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planemo upload for repository https://github.com/feltus/BDSS
author mingchen0919
date Mon, 11 Jun 2018 23:40:40 -0400
parents b12c945daf86
children 0d15928a648c
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b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
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1 # run job scripts within the tool outputs directory
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
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2 cd ${REPORT_FILES_PATH}
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a110308993be planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
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3 mkdir download_dir
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b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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a110308993be planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
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5 #========== build and run bdss-download.sh script ============
a110308993be planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
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6 echo 'export PATH=/main/sites/galaxy/galaxy/tools/_conda/bin:$PATH' > bdss-download.sh
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b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
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a110308993be planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
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8 echo 'for u in $(echo $X_u | sed "s/,/ /g");' >> bdss-download.sh
a110308993be planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
parents: 0
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9 echo 'do' >> bdss-download.sh
a110308993be planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
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10 echo ' bdss transfer --destination download_dir -u $u' >> bdss-download.sh
a110308993be planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
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11 echo 'done' >> bdss-download.sh
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b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
parents:
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b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
mingchen0919
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b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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14 sh bdss-download.sh