Mercurial > repos > mingchen0919 > aurora_htseq

annotate build-and-run-job-scripts.sh @ 18:0489a2fd17d6 draft

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planemo upload commit 389e632f9395db700c789034d9872c6b45a70b21-dirty
author mingchen0919
date Thu, 29 Nov 2018 15:01:19 -0500
parents ce76fb2791e5
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1 # run job scripts within the tool outputs directory
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2 cd ${REPORT_FILES_PATH}
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4 #========== build and run job 1 script ============
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5 cat >htseq-count.sh <<EOF
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6 htseq-count \\
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7 $(echo ${X_A} | sed 's/,/ /g') \\
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8 ${X_G} \\
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9 -f ${X_f} \\
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10 -r ${X_r} \\
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11 -s ${X_S} \\
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12 -a ${X_a} \\
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13 -t ${X_T} \\
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14 -i ${X_i} \\
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15 -m ${X_m} > htseq-counts-raw.txt
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17 grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' htseq-counts-raw.txt > counts.txt
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19 EOF
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21 # run job 1 script
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22 sh htseq-count.sh
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