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I think you are making a mistake in your Dockerfile. You cannot layer docker images the way you have tried.

I believe that when you have:

FROM ros:indigo-ros-core
LABEL maintainer "patlekano@gmail.com"

# install ros packages
RUN apt-get update && apt-get install -y \
    ros-indigo-ros-base=1.1.4-0* \
    && rm -rf /var/lib/apt/lists/*

# Install gazebo
FROM gazebo:gzserver6

FROM ubuntu:trusty

The image will actually only use ubuntu:trusy and 'forget' about the things you did before. You are probably best of starting from the image that has most of what you want, and then install the rest on top of it (using apt) it's a bit of a hassle, but I recently created a CUDA enabled trusty-ros-indigo-moveit image this way and it worked fine. I have removed a couple of things so not entirely certain but I think it should work like this. The entrypoint is the same as the one from indigo-ros-core.

FROM nvidia/cuda:8.0-devel-ubuntu14.04
# setup environment
RUN locale-gen en_US.UTF-8
ENV LANG en_US.UTF-8

# setup sources.list
RUN echo "deb http://packages.ros.org/ros/ubuntu trusty main" > /etc/apt/sources.list.d/ros-latest.list

# install bootstrap tools
RUN apt-get update && apt-get install --no-install-recommends -y \
    python-rosdep \
    python-rosinstall \
    python-vcstools \
    && rm -rf /var/lib/apt/lists/*

# bootstrap rosdep
RUN rosdep init \
    && rosdep update

# install ros packages
ENV ROS_DISTRO indigo
RUN apt-get update && apt-get install -y \
    ros-indigo-desktop-full=1.1.4-0* \
    && rm -rf /var/lib/apt/lists/*

# setup entrypoint
COPY ./ros_entrypoint.sh /

ENTRYPOINT ["/ros_entrypoint.sh"]
CMD ["bash"]

# ros-indigo-ros-base
RUN apt-get update && apt-get install -y \
    ros-indigo-ros-base=1.1.4-0* \
&& rm -rf /var/lib/apt/lists/*

# moveit-indigo-ci
ENV TERM xterm

# Setup catkin workspace
ENV CATKIN_WS=/root/ws_moveit
RUN mkdir -p $CATKIN_WS/src
WORKDIR $CATKIN_WS/src

# Commands are combined in single RUN statement with "apt/lists" folder removal to reduce image size
RUN wstool init . && \
    # Download moveit source so that we can get necessary dependencies
    wstool merge https://raw.githubusercontent.com/ros-planning/moveit/${ROS_DISTRO}-devel/moveit.rosinstall && \
    wstool update && \
    # Update apt-get because previous images clear this cache
    apt-get -qq update && \
    # Install some base dependencies
    apt-get -qq install -y \
        # Required for rosdep command
        sudo \
        # Required for installing dependencies
        python-rosdep \
        # Preferred build tool
        python-catkin-tools \
        # Not sure if necessary:
        ros-$ROS_DISTRO-rosbash \
        ros-$ROS_DISTRO-rospack && \
    # Download all dependencies of MoveIt!
    rosdep update && \
    rosdep install -y --from-paths . --ignore-src --rosdistro ${ROS_DISTRO} --as-root=apt:false && \
    # Remove the source code from this container. TODO: in the future we may want to keep this here for further optimization of later containers
    cd .. && \
    rm -rf src/ && \
    # Clear apt-cache to reduce image size
    rm -rf /var/lib/apt/lists/*

# Continous Integration Setting
ENV IN_DOCKER 1

# moveit-indigo-release
RUN apt-get update && \
    apt-get install -y \
        ros-${ROS_DISTRO}-moveit-* && \
rm -rf /var/lib/apt/lists/*

Hope this helps.