Dockerfile

FROM ubuntu:latest

MAINTAINER Yvan Le Bras "yvan.le-bras@mnhn.fr"

# From previous work from Valentin Chambon
# These environment variables are passed from Galaxy to the container
# and help you enable connectivity to Galaxy from within the container.
# This means your user can import/export data from/to Galaxy.

USER root
ENV DEBIAN_FRONTEND=noninteractive \
    API_KEY=none \
    DEBUG=false \
    PROXY_PREFIX=none \
    GALAXY_URL=none \
    GALAXY_WEB_PORT=10000 \
    HISTORY_ID=none \
    REMOTE_HOST=none

#Vim to modify ass porky
RUN apt-get update  && \
    apt-get install --no-install-recommends -y \
    wget python python-pip \
    openjdk-8-jdk vim unzip curl net-tools

ENV JAVA_HOME /usr/lib/jvm/java-8-openjdk-amd64
ENV PATH="/usr/lib/jvm/java-8-openjdk-amd64/bin:${PATH}"

RUN pip install setuptools && \
    pip install bioblend galaxy-ie-helpers && \
    pip install https://github.com/ValentinChCloud/urllib2_file/archive/master.tar.gz

# Download and "mount" OpenRefine
RUN wget -q -O - --no-check-certificate https://github.com/ValentinChCloud/OpenRefine/archive/master.tar.gz |tar -xz && \
    mv OpenRefine-master OpenRefine

# make some changes to Openrefine to export data to galaxy history
ADD ./ExportRowsCommand.java OpenRefine/main/src/com/google/refine/commands/project/ExportRowsCommand.java
ADD ./exporters.js OpenRefine/main/webapp/modules/core/scripts/project/exporters.js
ADD ./langs/translation-default.json OpenRefine/main/webapp/modules/core/langs/translation-default.json
ADD ./langs/translation-fr.json OpenRefine/main/webapp/modules/core/langs/translation-fr.json
ADD ./langs/translation-fr.json OpenRefine/main/webapp/modules/core/langs/translation-en.json

RUN /OpenRefine/refine build

#Get python api openrefine
RUN wget -q -O - --no-check-certificate https://github.com/maxogden/refine-python/archive/master.tar.gz | tar -xz && \
    mv refine-python-master refine-python

#Import data
ADD ./get_notebook.py /get_notebook.py

# not needed anymore
#ADD ./startup.sh /startup.sh

# Create and export project
ADD ./openrefine_create_project_API.py /refine-python/openrefine_create_project_API.py
ADD ./openrefine_export_project.py /refine-python/openrefine_export_project.py

# /import will be the universal mount-point for Jupyter
# The Galaxy instance can copy in data that needs to be present to the
# container
RUN mkdir /import

VOLUME ["/import"]
WORKDIR /import/

EXPOSE 3333