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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit ae672027942a606c1a5e302348279a5493151c11-dirty
author mvdbeek
date Fri, 08 Jul 2016 15:09:10 -0400
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1 # Script runner base image
2 #
3 # VERSION 0.3
4 # This Dockerfile is the base system for executing scripts with the docker scriptrunner.
5
6 FROM toolshed/requirements
7
8 MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com
9
10 # make sure the package repository is up to date
11 ENV DEBIAN_FRONTEND noninteractive
12 RUN apt-get -qq update
13
14 # Install all requirements that are recommend by the Galaxy project
15 RUN apt-get install -y --no-install-recommends imagemagick libfreetype6-dev wget curl \
16 libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev liblzma-dev \
17 libpcre3-dev libbz2-dev libx11-dev
18
19 RUN useradd galaxy --create-home --uid 1450 && \
20 chown -R galaxy:galaxy /home/galaxy/
21 USER galaxy
22 WORKDIR /home/galaxy
23 ENV CONDA_PREFIX="/home/galaxy/conda" \
24 PATH="/home/galaxy/conda/envs/default/bin:/home/galaxy/conda/bin:$PATH"
25
26 RUN curl https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -L -o miniconda.sh
27 RUN bash miniconda.sh -b -p "$CONDA_PREFIX" && rm miniconda.sh
28 RUN bash -c "conda create -y -q -c bioconda --name default samtools==0.1.19 bcftools && \
29 conda config --add channels r && \
30 conda config --add channels bioconda && \
31 conda config --add channels iuc && \
32 . activate default && \
33 conda install ghostscript"
34 CMD /bin/bash -c ". activate default && exec /bin/bash"