Mercurial > repos > drosofff > repenrich

view test-data/tool_wrapper.sh @ 4:d359ec9f0fe1 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit 0ec9810f3c05456fa8f19329a56eb1db32e218e5
author drosofff
date Tue, 30 May 2017 19:52:36 -0400
parents 54a3f3a195d6
children
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input_base=Samp
baseReference=chrM

bowtie-build ${baseReference}.fa ${baseReference}

python RepEnrich_setup.py ${baseReference}_repeatmasker.txt ${baseReference}.fa \
       setup_folder_${baseReference}

bowtie $baseReference -p 16 -t -m 1 -S --max ${input_base}_multimap.fastq \
       ${input_base}.fastq ${input_base}_unique.sam

samtools view -bS ${input_base}_unique.sam > ${input_base}_unique.bam
samtools sort ${input_base}_unique.bam ${input_base}_unique_sorted
mv ${input_base}_unique_sorted.bam ${input_base}_unique.bam
samtools index ${input_base}_unique.bam
rm ${input_base}_unique.sam

python RepEnrich.py ${baseReference}_repeatmasker.txt ${input_base} ${input_base} \
        setup_folder_${baseReference} ${input_base}_multimap.fastq ${input_base}_unique.bam --cpus 16