Mercurial > repos > mingchen0919 > aurora_htseq_site

annotate build-and-run-job-scripts.sh @ 0:dcf65671e56a draft

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 12:52:51 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
1 # run job scripts within the tool outputs directory
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
2 cd ${REPORT_FILES_PATH}
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
3
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
4 #========== build and run job 1 script ============
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
5 cat >htseq-count.sh <<EOF
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
6 htseq-count \\
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
7 $(echo ${X_A} | sed 's/,/ /g') \\
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
8 ${X_G} \\
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
9 -f ${X_f} \\
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
10 -r ${X_r} \\
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
11 -s ${X_S} \\
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
12 -a ${X_a} \\
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
13 -t ${X_T} \\
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
14 -i ${X_i} \\
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
15 -m ${X_m} > htseq-counts-raw.txt
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
16
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-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
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
18
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
19 EOF
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
20
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
21 # run job 1 script
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
22 sh htseq-count.sh
dcf65671e56a planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents:
diff changeset
23