Dockerfile to run planemo

Dockerfile.planemo

# ref: https://gist.github.com/eschen42/d5b7850ea74c6dd8f37714f7d48955fc

# Objective - To create a Docker environment in which I can run planemo
# To build 
#    sudo docker build -t eschen42/planemo .
# To run and delete the container on exit
#    sudo docker run --rm -ti eschen42/planemo
# You will be logged in as the 'debian' user without superuser privileges.
# For superuser privileges, supply arguments, e.g.:
#    sudo docker run --rm -ti eschen42/planemo bash -c "export TERM=xterm; /bin/bash"
#
# If you want persistent storage outside the container,
#    consider and understand the -v (--volume) option for 'docker run',
# e.g.,
#    mkdir ~/debhome; sudo docker run --rm -ti -v ~/debhome:/home/debian eschen42/planemo
# Note that this works best if your UID is the same as the debian user created here; 
#    if your UID is not 1000, change the "RUN groupadd ..." line to use your UID.

FROM debian:jessie
MAINTAINER Arthur C. Eschenlauer, esch0041@umn.edu

# explicitly set user/group IDs for debian user 
RUN groupadd -r debian --gid=1000 && useradd -s /bin/bash -m -g debian --uid=1000 debian

RUN apt-get update \
  && apt-get -y install bzip2 curl wget vim-tiny 
RUN update-alternatives --install /usr/bin/vim vim /usr/bin/vim.tiny 10
RUN apt-get -y install net-tools bind9-host dnsutils
RUN apt-get -y install locales gawk debconf git

RUN locale-gen en_US.UTF-8 && dpkg-reconfigure locales

RUN su -l -c '/bin/bash -c "curl -fsSL https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh > /home/debian/Miniconda2-installer-Linux-x86_64.sh"' debian
RUN su -l -c "chmod +x /home/debian/Miniconda2-installer-Linux-x86_64.sh" debian \
  && su -l -c "/home/debian/Miniconda2-installer-Linux-x86_64.sh -b" debian

RUN su -l -c "echo \"export PATH='/home/debian/miniconda2/bin:$PATH'\" >>~/.bash_profile" debian

RUN su -l -c "conda config --add channels r" debian
RUN su -l -c "conda config --add channels bioconda" debian
RUN su -l -c "conda install -c conda-forge pyaml" debian
RUN su -l -c "conda install planemo" debian

RUN echo '#!/usr/bin/env bash' > /entrypoint.sh \
 && echo "if [ \"'$1'\" = \"''\" ]; then su - debian; else $0; fi" >> /entrypoint.sh \
 && chmod +x /entrypoint.sh

RUN su -l -c "rm /home/debian/Miniconda2-installer-Linux-x86_64.sh" debian

CMD ["/usr/bin/env",  "bash", "/entrypoint.sh"]