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Last pushed: 2 years ago
Dockerfile
############################################################# # Dockerfile to build image for Bed to BigBed step in eoulsan # Based on Ubuntu ############################################################# # Set the base image to Ubuntu FROM ubuntu:14.04 # Update the repository sources list RUN apt-get update RUN apt-get -y install wget RUN apt-get -y install python RUN apt-get -y install gzip RUN apt-get -y install heimdall-flash heimdall-flash-frontend WORKDIR /tmp RUN wget http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedToBigBed RUN wget https://raw.githubusercontent.com/ENCODE-DCC/kentUtils/master/src/hg/lib/encode/narrowPeak.as RUN wget https://raw.githubusercontent.com/igvteam/igv/master/resources/chromSizes/mm10.chrom.sizes RUN wget https://genome.ucsc.edu/goldenPath/help/hg19.chrom.sizes RUN wget https://genome.ucsc.edu/goldenPath/help/hg38.chrom.sizes RUN chmod +x bedToBigBed RUN sed '13d' narrowPeak.as > broadPeak.as WORKDIR / RUN touch awkCommand.sh RUN printf "#!/bin/bash\n" >> awkCommand.sh RUN printf "awk 'NR == FNR {if(max < \$5) {max = \$5}; next} OFS=\"\t\" {\$5 = int(\$5 / max * 1000)}1' \$1 \$1 > \$2" >> awkCommand.sh RUN chmod +x awkCommand.sh
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