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# Dockerfile to build DELLY workflow container
# Based on Ubuntu
############################################################

# Set the base image to Ubuntu
FROM seqware/seqware_whitestar:1.1.1

# File Author / Maintainer
MAINTAINER Ivica Letunic <letunic@biobyte.de>

USER root
RUN apt-get -m update

RUN apt-get install -y apt-utils tar git curl nano wget dialog net-tools build-essential time
RUN apt-get install -y python python-dev python-distribute python-pip 
RUN apt-get install -y r-base r-base-dev
RUN apt-get install -y tabix cython
RUN pip install pybedtools numpy docopt PyVCF
RUN wget https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2 -O - |tar -xj -C /tmp/; cd /tmp/samtools-1.2; make; make install
#RUN echo "source(\"http://bioconductor.org/biocLite.R\")" > /tmp/dnacopy; echo "biocLite()" >> /tmp/dnacopy; R CMD BATCH /tmp/dnacopy
COPY scripts/* /usr/bin/
RUN for i in cleanup.sh cov cov_plot.pl cov_v0.5.6_linux_x86_64bit cov_v0.5.6_parallel_linux_x86_64bit delly delly_pcawg_qc_json.py delly_pcawg_timing_json.py delly_pe_dump.sh delly_prepare_uploader.sh DellySomaticFreqFilter.py delly_v0.6.3_parallel_linux_x86_64bit delly_v0.6.6_parallel_linux_x86_64bit dellyVcf2Tsv.py vcfcombine vcf_index.sh vcf-sort; do chmod a+rx /usr/bin/$i; done;
RUN echo 'install.packages("/usr/bin/DNAcopy_1.38.1.tar.gz")' >> /tmp/dnacopy; R CMD BATCH /tmp/dnacopy
COPY DELLY /home/seqware/DELLY
RUN chown -R seqware /home/seqware/DELLY
USER seqware
WORKDIR /home/seqware/DELLY/
RUN mvn clean install
CMD ["/bin/bash"]