Mercurial > repos > mingchen0919 > aurora_star
view build-and-run-job-scripts.sh @ 0:25602263cff0 draft default tip
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author | mingchen0919 |
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date | Sun, 30 Dec 2018 13:11:48 -0500 |
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# run SHELL_SCRIPT within tool outputs directory cd ${REPORT_FILES_PATH} #--------- job 1: index genome -------- # create genome directory for genome indexes mkdir -p ${X_d}/genomeDir cat >temp.sh <<EOF STAR \\ --runMode genomeGenerate \\ --genomeDir ${X_d}/genomeDir \\ --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\ --sjdbGTFfile ${X_B} \\ --sjdbOverhang ${X_C} \\ > genome-indexing.log.txt 2>&1 EOF grep -v None temp.sh > index-genome.sh # run star sh index-genome.sh #--------- job 2: mapping --------- cat >temp.sh <<EOF STAR \\ --genomeDir ${X_d}/genomeDir \\ --readFilesIn \\ ${X_F} \\ ${X_R} \\ > mapping.log.txt 2>&1 EOF grep -v None temp.sh > mapping.sh # remove temp.sh rm temp.sh # run mapping sh mapping.sh #--------- job 3: SAM to sorted BAM ------ echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh sh sam2bam.sh #--------- job 4: evaluate mapping ------- echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh sh flagstat.sh