Dockerfile

#    ______________________   ______     __
#   /  _/ ____/ ____/ ____/  / ____/__  / /_
#   / // /   / / __/ /      / / __/ _ \/ __/
# _/ // /___/ /_/ / /___   / /_/ /  __/ /_
#/___/\____/\____/\____/   \____/\___/\__/
# Banner @ http://goo.gl/VCY0tD

FROM       ubuntu:14.04
MAINTAINER ICGC <dcc-support@icgc.org>

ENV EGA_VERSION 2.2.2
ENV GT_VERSION 3.8.7
ENV GT_VERSION_LONG 207
ENV GDC_VERSION gdc-client_v1.3.0_Ubuntu14.04_x64


#
# Update apt, add FUSE support, required libraries and basic command line tools
#

RUN apt-get update && \
    apt-get -y upgrade && \
    apt-get install -y libfuse-dev fuse software-properties-common && \
    apt-get install -y python-pip python-dev libffi-dev && \
# Required to install clients
    apt-get install -y unzip curl wget && \
# Required for Genetorrent and icgc
    apt-get install -y libicu52 && \
# Required to download Genetorrent
    apt-get install -y  openssl libssl-dev && \
# Required for addressing ownership of files created by root
    apt-get install -y inotify-tools


#
# Install Oracle JDK 8 for icgc storage client, ega
#

RUN add-apt-repository ppa:webupd8team/java
RUN apt-get update && apt-get upgrade -y
RUN echo oracle-java8-installer shared/accepted-oracle-license-v1-1 select true | /usr/bin/debconf-set-selections
RUN apt-get install -y \
    oracle-java8-installer \
    oracle-java8-set-default
ENV JAVA_HOME /usr/lib/jvm/java-8-oracle

#
# Download and install latest EGA download client version
#

RUN mkdir -p /icgc/ega-download-demo && \
    cd /icgc/ega-download-demo && \
    wget -qO- https://www.ebi.ac.uk/ega/sites/ebi.ac.uk.ega/files/documents/EgaDemoClient_$EGA_VERSION.zip -O temp.zip ; \
    unzip temp.zip -d /icgc/ega-download-demo

#
# Install GeneTorrent and add to PATH
#

RUN mkdir -p /icgc/genetorrent && \
    cd /icgc/genetorrent && \
    wget -qO- https://annai.egnyte.com/dd/LWTWQGXeAi/ -O genetorrent-download.deb && \
    wget -qO- https://annai.egnyte.com/dd/Ixrj77etn2 -O genetorrent-common.deb && \
    apt-get install libboost-filesystem1.54.0 libboost-program-options1.54.0 libboost-regex1.54.0 libboost-system1.54.0 libxerces-c3.1 libxqilla6 python-support &&\
    dpkg -i ./genetorrent-common.deb && \
    dpkg -i ./genetorrent-download.deb

ENV PATH=$PATH:/icgc/genetorrent/bin

# 
# Install latest version of storage client distribution, import modified logback file
#

RUN mkdir -p /icgc/score-client && \
    cd /icgc/score-client && \
    wget -qO- 'https://artifacts.oicr.on.ca/artifactory/dcc-release/bio/overture/score-client/[RELEASE]/score-client-[RELEASE]-dist.tar.gz' | \
    tar xvz --strip-components 1 && \
    mkdir -p /icgc/score-client/logs && \
    chmod a+w /icgc/score-client/logs && \
    mkdir -p /icgc/proxy

COPY ./logback.xml /icgc/score-client/conf

COPY ./icgc-storage-client-proxy.sh /icgc/proxy/icgc-storage-client-proxy
RUN chmod og+x /icgc/proxy/icgc-storage-client-proxy

#
# Install latest version of gdc download tool
#

RUN mkdir -p /icgc/gdc-data-transfer-tool && \
    cd /icgc/gdc-data-transfer-tool && \
    wget -qO- https://gdc.cancer.gov/system/files/authenticated%20user/0/$GDC_VERSION.zip -O temp.zip ; \
    unzip temp.zip -d /icgc/gdc-data-transfer-tool ; \
    rm temp.zip && \
    cd /icgc

ENV PATH=$PATH:/icgc/gdc-data-transfer-tool

#
# Install icgc-get for development purposes and make mount point directory, install aws-cli, cleanup pip
#

RUN export DEBIAN_FRONTEND=noninteractive && \
    apt-get upgrade -y && \
    pip install -U pip setuptools && \
    pip install pyyaml && \
    pip install awscli && \
    pip uninstall -y pip setuptools && \
    mkdir /icgc/mnt 

#
# Set working directory for convenience with interactive usage, copy icgc-get for development purposes
#

WORKDIR /icgc