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Add Docker files to build v1.0.2 image.
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FROM ubuntu:18.04 | ||
MAINTAINER Jonathan Crabtree <jcrabtree@som.umaryland.edu> | ||
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RUN apt-get update && apt-get install -y curl | ||
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# Perl dependencies | ||
RUN apt-get install -y libgd-svg-perl libjson-perl libtext-csv-perl liblog-log4perl-perl vcftools libbatik-java libmodule-build-perl make cpanminus bioperl fop | ||
RUN cpanm Bio::FeatureIO::gff | ||
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# Install specific release of Circleator from source | ||
RUN cd /opt && curl -LO https://github.com/jonathancrabtree/Circleator/archive/1.0.2.tar.gz && tar xzf 1.0.2.tar.gz | ||
RUN cd /opt/Circleator-1.0.2 && perl Build.PL && ./Build && ./Build install | ||
RUN cd /opt && ln -s Circleator-1.0.2 Circleator | ||
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# Install Circleator from GitHub master branch | ||
#RUN head -c 5 /dev/random >random2.txt && cd /opt && curl -LO https://github.com/jonathancrabtree/Circleator/archive/master.zip && unzip master.zip | ||
#RUN cd /opt/Circleator-master && perl Build.PL && ./Build && ./Build install | ||
#RUN cd /opt && ln -s Circleator-master Circleator | ||
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# bam_get_coverage (optional Circleator extra) | ||
# samtools 1.7 from source | ||
RUN apt-get install -y libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev gcc libglib2.0-dev | ||
RUN cd /opt && curl -LO https://github.com/samtools/samtools/releases/download/1.7/samtools-1.7.tar.bz2 && tar xjf samtools-1.7.tar.bz2 | ||
RUN cd /opt/samtools-1.7 && ./configure && make | ||
RUN cd /opt/Circleator/util/samtools && ./make.sh && cp bam_get_coverage *.pl ../*.pl /usr/local/bin/ | ||
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# add non-root user | ||
RUN useradd -ms /bin/bash circleator | ||
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# install tutorials in /home/circleator | ||
RUN cd /opt && curl -LO https://github.com/jonathancrabtree/Circleator/archive/gh-pages.zip && unzip gh-pages.zip | ||
RUN cp -r /opt/Circleator-gh-pages/tutorials /home/circleator/ && chown -R circleator:circleator /home/circleator/tutorials | ||
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# cleanup | ||
RUN /bin/rm -rf /opt/Circleator-gh-pages /opt/*.gz /opt/*.zip /opt/*.bz2 | ||
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# switch user | ||
USER circleator | ||
WORKDIR /home/circleator | ||
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#!/bin/bash | ||
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docker build -t umigs/circleator-v1.0.2 . |
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#!/bin/bash | ||
docker run -dt --name 'c1' umigs/circleator-v1.0.2:latest | ||
docker exec -i -t c1 /bin/bash |