Mercurial > repos > mingchen0919 > aurora_fastqc_site

comparison build-and-run-job-scripts.sh @ 8:94762f1cb779 draft

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planemo upload commit 76f9ca75d5b1c0c0fad6c10876d9dfeba7d5ecff-dirty
author mingchen0919
date Mon, 30 Apr 2018 16:15:39 -0400
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7:3f92c10de274 8:94762f1cb779
1 # run SHELL_SCRIPT within tool outputs directory
2 cd ${REPORT_FILES_PATH}
3
4 # build job-script.sh
5 cat >temp.sh <<EOF
6
7 cp ${X_r} read_1.fq
8 cp ${X_R} read_2.fq
9
10 fastqc \\
11 -q \\
12 -c ${X_c} \\
13 -l ${X_l} \\
14 ${X_d}/read_1.fq > read_1.log.txt 2>&1
15
16 fastqc \\
17 -q \\
18 -c ${X_c} \\
19 -l ${X_l} \\
20 ${X_d}/read_2.fq > read_2.log.txt 2>&1
21
22 EOF
23
24 grep -v None temp.sh > job-1-script.sh
25 rm temp.sh
26
27 # run SHELL_SCRIPT
28 sh job-1-script.sh
29
30 # unzip outputs
31 unzip -q read_1_fastqc.zip
32 unzip -q read_2_fastqc.zip