Mercurial > repos > mingchen0919 > aurora_star_site

comparison build-and-run-job-scripts.sh @ 0:c12e291895ff draft

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planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
author mingchen0919
date Tue, 01 May 2018 10:45:22 -0400
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-1:000000000000 0:c12e291895ff
1 # run SHELL_SCRIPT within tool outputs directory
2 cd ${REPORT_FILES_PATH}
3
4 #--------- job 1: index genome --------
5 # create genome directory for genome indexes
6 mkdir -p ${X_d}/genomeDir
7
8 cat >temp.sh <<EOF
9 STAR \\
10 --runMode genomeGenerate \\
11 --genomeDir ${X_d}/genomeDir \\
12 --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\
13 --sjdbGTFfile ${X_B} \\
14 --sjdbOverhang ${X_C} \\
15 > genome-indexing.log.txt 2>&1
16 EOF
17
18 grep -v None temp.sh > index-genome.sh
19
20 # run star
21 sh index-genome.sh
22
23 #--------- job 2: mapping ---------
24 cat >temp.sh <<EOF
25 STAR \\
26 --genomeDir ${X_d}/genomeDir \\
27 --readFilesIn \\
28 ${X_F} \\
29 ${X_R} \\
30 > mapping.log.txt 2>&1
31 EOF
32
33 grep -v None temp.sh > mapping.sh
34
35 # remove temp.sh
36 rm temp.sh
37
38 # run mapping
39 sh mapping.sh
40
41
42
43 #--------- job 3: SAM to sorted BAM ------
44 echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh
45 sh sam2bam.sh
46
47 #--------- job 4: evaluate mapping -------
48 echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh
49 sh flagstat.sh