Mercurial > repos > mingchen0919 > aurora_skewer

annotate shell-script-template.sh @ 6:5b07e567864b draft

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planemo upload commit ee93fa730d90ffc1a895a849bdcb6050ed5ad2c9-dirty
author mingchen0919
date Wed, 25 Apr 2018 17:20:11 -0400
parents 2c663ddb8488
children c5c297020c36
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1 # run SHELL_SCRIPT within tool outputs directory
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2 cd ${REPORT_FILES_PATH}
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4 #--------- index genome --------
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5 # create genome directory for genome indexes
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6 mkdir -p ${X_d}/genomeDir
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8 cat >temp.sh <<EOF
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9 STAR \\
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10 --runMode genomeGenerate \\
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11 --genomeDir ${X_d}/genomeDir \\
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12 --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \\
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13 --sjdbGTFfile ${X_B} \\
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14 --sjdbOverhang ${X_C} \\
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15 > /dev/null 2>&1
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16 EOF
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18 grep -v None temp.sh > index-genome.sh
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20 # run star
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21 sh index-genome.sh
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23 #---- mapping ---------
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24 cat >temp.sh <<EOF
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25 STAR \\
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26 --genomeDir ${X_d}/genomeDir \\
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27 --readFilesIn \\
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28 ${X_F} \\
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29 ${X_R} \\
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30 > /dev/null 2>&1
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31 EOF
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33 grep -v None temp.sh > mapping.sh
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35 # run mapping
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36 sh mapping.sh
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38 # remove temp.sh
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39 rm temp.sh
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41 #----- SAM to sorted BAM ------
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42 echo "samtools sort -o Aligned.out.sorted.bam Aligned.out.sam" > sam2bam.sh
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43 sh sam2bam.sh
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45 #----- evaluate mapping -------
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46 echo "samtools flagstat Aligned.out.sorted.bam > flagstat.txt" > flagstat.sh
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47 sh flagstat.sh