Mercurial > repos > mvdbeek > docker_toolfactory_alpha
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Allow whitespace in gene name and fix missing creation of output section.
author | mvdbeek |
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date | Wed, 14 Jan 2015 17:19:16 +0100 |
parents | 477eac6c4cea |
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# Toolfactory image # # VERSION 0.1 # This Dockerfile is the base system for executing scripts by the DockerToolFactory. FROM debian:jessie 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 --no-install-recommends -y autoconf automake build-essential gfortran \ cmake git-core libatlas-base-dev libblas-dev liblapack-dev mercurial subversion python-dev \ pkg-config openjdk-7-jre python-setuptools adduser zlib1g-dev ghostscript r-base-core \ graphicsmagick-imagemagick-compat RUN apt-get install -y python-virtualenv libfreetype6-dev exonerate bedtools wget curl \ libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev samtools liblzma-dev \ libpcre3-dev libbz2-dev RUN easy_install pip RUN pip install numpy pysam tornado matplotlib pip pandas ipython rpy2 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("DESeq", "DESeq2", "edgeR", "EDASeq"))' RUN Rscript -e 'install.packages(c("latticeExtra", "ggplot2", "reshape", "gridExtra"), dependencies=TRUE, repos="http://cran.us.r-project.org")' RUN apt-get install bc RUN easy_install intermine #add galaxy user (could be any username). #1001 will be replaced by the actual user id of the system user #executing the galaxy tool, so that file write operations are possible. RUN adduser galaxy -u 1002 RUN usermod -aG staff galaxy #VOLUME ["/home/galaxy/"] RUN mkdir /home/galaxy/job_working_directory WORKDIR /home/galaxy/job_working_directory USER galaxy #ENTRYPOINT chown -R galaxy /home/galaxy/ && su - galaxy CMD /bin/bash