Mercurial > repos > mingchen0919 > aurora_fastqc_site

annotate build-and-run-job-scripts.sh @ 2:c64267b9f754 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 12:48:14 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
1 # run SHELL_SCRIPT within tool outputs directory
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
2 cd ${REPORT_FILES_PATH}
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
3
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
4 # build job-script.sh
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
5 cat >temp.sh <<EOF
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
6
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
7 cp ${X_r} read_1.fq
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
8 cp ${X_R} read_2.fq
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
9
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
10 fastqc \\
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
11 -q \\
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
12 -c ${X_c} \\
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
13 -l ${X_l} \\
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
14 ${X_d}/read_1.fq > read_1.log.txt 2>&1
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
15
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
16 fastqc \\
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
17 -q \\
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
18 -c ${X_c} \\
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
19 -l ${X_l} \\
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
20 ${X_d}/read_2.fq > read_2.log.txt 2>&1
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
21
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
22 EOF
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
23
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
24 grep -v None temp.sh > job-1-script.sh
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
25 rm temp.sh
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
26
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
27 # run SHELL_SCRIPT
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
28 sh job-1-script.sh
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
29
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
30 # unzip outputs
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
31 unzip -q read_1_fastqc.zip
c64267b9f754 planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
32 unzip -q read_2_fastqc.zip