Mercurial > repos > mingchen0919 > aurora_htseq

annotate build-and-run-job-scripts.sh @ 1:fd547674f29f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1-dirty
author mingchen0919
date Thu, 13 Dec 2018 23:10:32 -0500
parents 803f4888f36a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
1 # run job scripts within the tool outputs directory
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
2 cd ${REPORT_FILES_PATH}
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
3
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
4 #========== build and run job 1 script ============
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
5 cat >htseq-count.sh <<EOF
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
6 htseq-count \\
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
7 $(echo ${X_A} | sed 's/,/ /g') \\
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
8 ${X_G} \\
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
9 -f ${X_f} \\
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
10 -r ${X_r} \\
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
11 -s ${X_S} \\
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
12 -a ${X_a} \\
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
13 -t ${X_T} \\
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
14 -i ${X_i} \\
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
15 -m ${X_m} > htseq-counts-raw.txt
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
16
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
17 grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' htseq-counts-raw.txt > counts.txt
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
18
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
19 EOF
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
20
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
21 # run job 1 script
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
22 sh htseq-count.sh
803f4888f36a planemo upload commit 004a320fc0619c234164b44c64ba5dce205734e1
mingchen0919
parents:
diff changeset
23