Dockerfile

#  Copyright (c) 2014-2018, Centre for Genomic Regulation (CRG).
#  Copyright (c) 2014-2018, Jose Espinosa-Carrasco and the respective authors.
#
#  This file is part of Pergola.
#
#  Pergola is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
#
#  Pergola is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  You should have received a copy of the GNU General Public License
#  along with Pergola.  If not, see <http://www.gnu.org/licenses/>.
#
############################################################
# Dockerfile to build Pergola with all its dependencies
# Based on ubuntu xenial
############################################################

## Set the base image to debian wheezy
# FROM debian:wheezy
# 7 corresponds to wheezy, this way I control the exact release
# FROM debian:7.11

## Set the base image to ubuntu xenial
FROM ubuntu:16.04

MAINTAINER Jose Espinosa-Carrasco <espinosacarrascoj@gmail.com>

## Install Python and Basic Python Tools

## Update always before download
# single command save space, because each run generates a folder layer
RUN apt-get update && \
    apt-get install -y python \
    python-dev \
    python-distribute \
    python-pip \
    gfortran \
    libblas-dev \
    liblapack-dev \
    bedtools \
    bzip2 \
    liblzma-dev \
    zlibc \
    libbz2-dev \
    zlib1g-dev \
    libhdf5-dev

## Copying pergola
COPY pergola /pergola/pergola
COPY requirements.txt /pergola/
COPY setup.py /pergola/
COPY README.md /pergola/

## TODO add requirements.txt file to pergola
RUN pip install -r /pergola/requirements.txt && \
    pip install cython && \
    pip install h5py && \
    cd pergola && python setup.py install