Mercurial > repos > mingchen0919 > aurora_bdss_url

annotate build-and-run-job-scripts.sh @ 0:b12c945daf86 draft

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planemo upload for repository https://github.com/feltus/BDSS
author mingchen0919
date Mon, 11 Jun 2018 23:04:53 -0400
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children a110308993be
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b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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1 # run job scripts within the tool outputs directory
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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2 cd ${REPORT_FILES_PATH}
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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3
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4 #========== build and run job 1 script ============
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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5 cat >bdss-download.sh <<EOF
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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6 #------------ BELOW IS WHERE YOU WRITE YOUR OWN SHELL SCRIPT --------------
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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7 export PATH=/main/sites/galaxy/galaxy/tools/_conda/bin:$PATH
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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8
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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9 for $u in $(echo $X_u | sed "s/,/ /g");
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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10 do
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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11 echo "bdss transfer --destination download_dir -u $u"
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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12 done
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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15 #------------ END OF SHELL SCRIPT ------------------------------------------
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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16 EOF
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b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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18
b12c945daf86 planemo upload for repository https://github.com/feltus/BDSS
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19 sh bdss-download.sh