Mercurial > repos > mingchen0919 > aurora_htseq_site

annotate build-and-run-job-scripts.sh @ 10:ee79ca0002b4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 363ef0a73d874c67326a67f51a78328906951248-dirty
author mingchen0919
date Fri, 30 Nov 2018 22:17:33 -0500
parents b3e5f4753856
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
1 # run job scripts within the tool outputs directory
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
2 cd ${REPORT_FILES_PATH}
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
3
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
4 #========== build and run job 1 script ============
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
5 cat >htseq-count.sh <<EOF
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
6 htseq-count \\
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
7 $(echo ${X_A} | sed 's/,/ /g') \\
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
8 ${X_G} \\
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
9 -f ${X_f} \\
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
10 -r ${X_r} \\
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
11 -s ${X_S} \\
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
12 -a ${X_a} \\
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
13 -t ${X_T} \\
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
14 -i ${X_i} \\
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
15 -m ${X_m} > htseq-counts-raw.txt
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
16
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
17 grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' htseq-counts-raw.txt > counts.txt
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
18
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
19 EOF
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
20
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
21 # run job 1 script
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
22 sh htseq-count.sh
b3e5f4753856 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents:
diff changeset
23