Mercurial > repos > mvdbeek > docker_scriptrunner
diff dockerfiles/scriptrunner/Dockerfile @ 0:21d312776891 draft
planemo upload for repository https://github.com/mvdbeek/docker_scriptrunner/ commit 30f8264cdd67d40dec8acde6407f32152e6a29c1-dirty
| author | mvdbeek |
|---|---|
| date | Sat, 09 Jul 2016 16:57:13 -0400 |
| parents | |
| children | 495946ffc2d6 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dockerfiles/scriptrunner/Dockerfile Sat Jul 09 16:57:13 2016 -0400 @@ -0,0 +1,38 @@ +# Script runner base image +# +# VERSION 0.3 +# This Dockerfile is the base system for executing scripts with the docker scriptrunner. + +FROM toolshed/requirements + +MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com + +# make sure the package repository is up to date +ENV DEBIAN_FRONTEND noninteractive +RUN apt-get -qq update + +# Install all requirements that are recommend by the Galaxy project +RUN apt-get install -y --no-install-recommends bc imagemagick libfreetype6-dev wget curl \ +libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev liblzma-dev \ +libpcre3-dev libbz2-dev libx11-dev + +RUN mkdir /var/home && \ + useradd galaxy --create-home --home-dir /home/galaxy --uid 1450 && \ + chown -R galaxy:galaxy /home/galaxy/ +USER galaxy +WORKDIR /home/galaxy +ENV CONDA_PREFIX="/home/galaxy/conda" \ + PATH="/home/galaxy/conda/envs/default/bin:/home/galaxy/conda/bin:$PATH" + +RUN curl https://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -L -o miniconda.sh +RUN bash miniconda.sh -b -p "$CONDA_PREFIX" && rm miniconda.sh +RUN bash -c "conda create -y -q -c bioconda --name default samtools==0.1.19 bcftools && \ + conda config --add channels r && \ + conda config --add channels bioconda && \ + conda config --add channels iuc && \ + . activate default && \ + conda install ghostscript coreutils" +USER root +RUN chown -R galaxy:users /home/galaxy && \ + chmod g=rwx /home/galaxy && \ + usermod -G users galaxy