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Dockerfile
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FROM pancancer/seqware_whitestar_pancancer:1.1.2-actual-java8
MAINTAINER Solomon Shorser <solomon.shorser@oicr.on.ca>
ENV OXOG_WRAPPER_IMAGE_VERSION 3.0.2
LABEL OXOG_WRAPPER_IMAGE_VERSION $OXOG_WRAPPER_IMAGE_VERSION
# For the storage client.
ENV STORAGE_PROFILE=collab
# OxoG Workflow needs tabix, bgzip and samtools
RUN sudo apt-get update && \
sudo apt-get install -y tabix samtools libstring-random-perl
USER root
#Next, Add the workflow and compile.
WORKDIR /home/seqware
RUN mkdir /home/seqware/OxoGWrapperWorkflowCode
COPY ./src /home/seqware/OxoGWrapperWorkflowCode/src
COPY ./links /home/seqware/OxoGWrapperWorkflowCode/links
COPY ./pom.xml /home/seqware/OxoGWrapperWorkflowCode/pom.xml
COPY ./workflow /home/seqware/OxoGWrapperWorkflowCode/workflow
COPY ./workflow.properties /home/seqware/OxoGWrapperWorkflowCode/workflow.properties
WORKDIR /home/seqware/OxoGWrapperWorkflowCode/
RUN mvn clean compile package install
#Link the newly built workflow into /workflows
USER root
RUN mkdir /workflows && \
ln -s $(pwd)/target/Workflow_Bundle_OxoGWrapper_${OXOG_WRAPPER_IMAGE_VERSION}_SeqWare_1.1.2/Workflow_Bundle_OxoGWrapper \
/workflows/Workflow_Bundle_OxoGWrapper
USER seqware
# Maybe make an entry point to run the workflow?