Dockerfile

# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

FROM java:openjdk-8-jre

# Install python
RUN apt-get update && \
    apt-get install python --yes && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

# Install gcloud
# See https://cloud.google.com/sdk/
RUN curl https://sdk.cloud.google.com | bash

# Add the install location explicitly to the path (for non-interactive shells)
ENV PATH /root/google-cloud-sdk/bin:$PATH

# Install pip for the next two steps...
RUN apt-get update && \
    apt-get install python-pip --yes

# Install Python "requests" (for cromwell_driver.py) package
RUN pip install requests simplejson

# Install Google Python client (for file_util.py) package
RUN pip install --upgrade google-api-python-client

# Remove pip
RUN apt-get remove --yes python-pip && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

# Copy the wdl_runner python, shell script, and dependencies
RUN mkdir /wdl_runner
COPY cromwell_driver.py \
     file_util.py \
     sys_util.py \
     wdl_outputs_util.py \
     wdl_runner.py \
     wdl_runner.sh \
     /wdl_runner/
RUN chmod u+x /wdl_runner/wdl_runner.sh

# Copy Cromwell and the Cromwell conf template
RUN mkdir /cromwell
RUN cd /cromwell && \
    curl -L -O https://github.com/broadinstitute/cromwell/releases/download/26/cromwell-26.jar
RUN ln /cromwell/cromwell-26.jar /cromwell/cromwell.jar
COPY jes_template.conf /cromwell/

# Set up the runtime environment
ENV CROMWELL /cromwell/cromwell.jar
ENV CROMWELL_CONF /cromwell/jes_template.conf

WORKDIR /wdl_runner