Mercurial > repos > mingchen0919 > aurora_star

annotate build-and-run-job-scripts.sh @ 13:6de40bffd5e3 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 09b6a41798350090b61aea16966ba64b583ef02b-dirty
author mingchen0919
date Sat, 09 Jun 2018 23:40:45 -0400
parents c77775cc4ecf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
1 # run SHELL_SCRIPT within tool outputs directory
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
2 cd ${REPORT_FILES_PATH}
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
3
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
4 #--------- job 1: index genome --------
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
5 # create genome directory for genome indexes
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
6 mkdir -p ${X_d}/genomeDir
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
7
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
8 cat >temp.sh <<EOF
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
9 STAR \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
10 --runMode genomeGenerate \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
11 --genomeDir ${X_d}/genomeDir \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
12 --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
13 --sjdbGTFfile ${X_B} \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
14 --sjdbOverhang ${X_C} \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
15 > genome-indexing.log.txt 2>&1
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
16 EOF
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
17
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
18 grep -v None temp.sh > index-genome.sh
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
19
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
20 # run star
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
21 sh index-genome.sh
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
22
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
23 #--------- job 2: mapping ---------
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
24 cat >temp.sh <<EOF
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
25 STAR \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
26 --genomeDir ${X_d}/genomeDir \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
27 --readFilesIn \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
28 ${X_F} \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
29 ${X_R} \\
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
30 > mapping.log.txt 2>&1
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
31 EOF
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
32
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
33 grep -v None temp.sh > mapping.sh
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
34
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
35 # remove temp.sh
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
36 rm temp.sh
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
37
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
38 # run mapping
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
39 sh mapping.sh
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
40
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
41
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
42
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
43 #--------- job 3: SAM to sorted BAM ------
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
44 echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
45 sh sam2bam.sh
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
46
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
47 #--------- job 4: evaluate mapping -------
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
48 echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh
c77775cc4ecf planemo upload commit d28f1764ef50ca42f996cada585cfcea9ec04e5a
mingchen0919
parents:
diff changeset
49 sh flagstat.sh