comparison build-and-run-job-scripts.sh @ 0:0358f6f78adf draft

planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Fri, 14 Dec 2018 00:40:15 -0500
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-1:000000000000 0:0358f6f78adf
1 # run job scripts within the tool outputs directory
2 cd ${REPORT_FILES_PATH}
3
4 #========== build and run job 1 script ============
5 cat >temp.sh <<EOF
6 skewer \\
7 ${X_A} \\
8 ${X_B} \\
9 -x ${X_x} \\
10 -y ${X_y} \\
11 -m ${X_m} \\
12 -r ${X_r} \\
13 -d ${X_D} \\
14 -q ${X_q} \\
15 -Q ${X_Q} \\
16 -l ${X_l} \\
17 -j ${X_j} \\
18 -M ${X_M} \\
19 -b ${X_b} \\
20 -c ${X_b} \\
21 -n ${X_n} \\
22 -u ${X_u} \\
23 -f ${X_f} \\
24 -z ${X_z} \\
25 -qiime ${X_E} \\
26 -quiet ${X_F} \\
27 -i ${X_i} \\
28 -o trim > skewer.log.txt 2>&1
29 EOF
30
31 # remove empty input lines
32 grep -v '\-M \\' temp.sh |\
33 grep -v 'None' |\
34 grep -v 'NO_ARGUMENT_NO' |\
35 sed 's/NO_ARGUMENT_YES//g' > job-1-script.sh
36
37 rm temp.sh
38
39 # run job 1 script
40 sh job-1-script.sh
41
42 # rename log file
43 if [ -e trim-trimmed.log ]; then
44 cp trim-trimmed.log trim-trimmed.txt
45 fi