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Dockerfile.txt
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Dockerfile.txt
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FROM ubuntu
### Install linux dependencies
RUN apt-get -y update
RUN apt -y install gcc
RUN apt-get install -y zlib1g-dev
RUN apt-get install -y libbz2-dev
RUN apt-get install -y liblzma-dev
RUN apt install -y make
### Install JRE, bgzip
RUN apt install -y openjdk-11-jre-headless
RUN apt install -y tabix
### bcftools (v 1.7), vcftools (v 0.1.15), Python2, pip, numpy, pandas and pyVCF
RUN apt install -y bcftools
RUN apt install -y vcftools
#RUN add-apt-repository -y universe
RUN apt install -y python2
RUN apt install -y curl
RUN curl https://bootstrap.pypa.io/pip/2.7/get-pip.py --output get-pip.py
RUN python2 get-pip.py
RUN pip2 install numpy
RUN pip2 install pandas
RUN pip2 install PyVCF
## Add bash scripts
RUN mkdir -p /usr/src/TrioSim
RUN mkdir -p /usr/src/TrioSim/jars
RUN mkdir -p /usr/src/TrioSim/data_files
ADD ./TrioSim.sh /usr/src/TrioSim/TrioSim.sh
ADD ./Offspring_VCF_creator.py /usr/src/TrioSim/Offspring_VCF_creator.py
ADD ./Offspring_VCF_generator.sh /usr/src/TrioSim/Offspring_VCF_generator.sh
ADD ./Parental_VCF_generator.sh /usr/src/TrioSim/Parental_VCF_generator.sh
ADD ./spikeIn_denovo_mutations.py /usr/src/TrioSim/spikeIn_denovo_mutations.py
ADD jars/simdrom-cli-0.0.2.jar /usr/src/TrioSim/jars/simdrom-cli-0.0.2.jar
ADD data_files/ALL.WGS_GRCh38_sites.20170504.vcf.gz /usr/src/TrioSim/data_files/ALL.WGS_GRCh38_sites.20170504.vcf.gz
ADD data_files/ALL.WGS_GRCh38_sites.20170504.vcf.gz.tbi /usr/src/TrioSim/data_files/ALL.WGS_GRCh38_sites.20170504.vcf.gz.tbi
ADD data_files/chr22_hg38_sites.vcf /usr/src/TrioSim/data_files/chr22_hg38_sites.vcf
ADD data_files/chromosome_name.txt /usr/src/TrioSim/data_files/chromosome_name.txt
ADD data_files/denovo-db.non-ssc-samples.chr22.UCSC_SNP_INDEL.vcf /usr/src/TrioSim/data_files/denovo-db.non-ssc-samples.chr22.UCSC_SNP_INDEL.vcf
ADD data_files/denovo-db.non-ssc-samples.variants_hg38LiftedOver_decoy_hla_UCSC_SNP_INDEL.vcf /usr/src/TrioSim/data_files/denovo-db.non-ssc-samples.variants_hg38LiftedOver_decoy_hla_UCSC_SNP_INDEL.vcf
RUN chmod +x /usr/src/TrioSim/TrioSim.sh
RUN chmod +x /usr/src/TrioSim/Offspring_VCF_creator.py
RUN chmod +x /usr/src/TrioSim/Offspring_VCF_generator.sh
RUN chmod +x /usr/src/TrioSim/Parental_VCF_generator.sh
RUN chmod +x /usr/src/TrioSim/spikeIn_denovo_mutations.py
RUN chmod +x /usr/src/TrioSim/spikeIn_denovo_mutations.py
## Execution command
WORKDIR /usr/src/TrioSim
ENTRYPOINT ["/usr/src/TrioSim/./TrioSim.sh"]