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planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
author mvdbeek
date Sat, 09 Jul 2016 16:57:13 -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 bc 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 mkdir /var/home && \
20 useradd galaxy --create-home --home-dir /home/galaxy --uid 1450 && \
21 chown -R galaxy:galaxy /home/galaxy/
22 USER galaxy
23 WORKDIR /home/galaxy
24 ENV CONDA_PREFIX="/home/galaxy/conda" \
25 PATH="/home/galaxy/conda/envs/default/bin:/home/galaxy/conda/bin:$PATH"
26
27 RUN curl https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -L -o miniconda.sh
28 RUN bash miniconda.sh -b -p "$CONDA_PREFIX" && rm miniconda.sh
29 RUN bash -c "conda create -y -q -c bioconda --name default samtools==0.1.19 bcftools && \
30 conda config --add channels r && \
31 conda config --add channels bioconda && \
32 conda config --add channels iuc && \
33 . activate default && \
34 conda install ghostscript coreutils"
35 USER root
36 RUN chown -R galaxy:users /home/galaxy && \
37 chmod g=rwx /home/galaxy && \
38 usermod -G users galaxy