jfroula/snp_hudson repository overview

FROM continuumio/miniconda2

RUN conda install -c bioconda gnuplot==5.0.4
RUN conda install -c conda-forge libgd==2.2.5
RUN conda install -c bioconda blat=35
RUN conda install -c bioconda bwa==0.7.15
RUN conda install -c bioconda picard==2.17.2
RUN conda install -c bioconda samtools==0.1.19
RUN conda install -c conda-forge numpy==1.14.0

# installing gatk
COPY GenomeAnalysisTK-3.6-0-g89b7209.tar.bz2 /root/GenomeAnalysisTK-3.6-0-g89b7209.tar.bz2
RUN conda install -c bioconda gatk==3.6
RUN bash /opt/conda/bin/gatk-register /root/GenomeAnalysisTK-3.6-0-g89b7209.tar.bz2