Mercurial > repos > mvdbeek > docker_toolfactory
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planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
author | mvdbeek |
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date | Sat, 03 Oct 2015 08:34:39 -0400 |
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# Toolfactory image # # VERSION 0.2 # This Dockerfile is the base system for executing scripts by the DockerToolFactory. 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 #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 1000 ADD adduser.sh /usr/local/bin/adduser.sh RUN adduser.sh RUN ulimit -n 1024 && apt-get update -qq && apt-get install -y --no-install-recommends software-properties-common && apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E084DAB9 && add-apt-repository \ "deb http://cran.irsn.fr/bin/linux/ubuntu trusty/" && apt-get update -qq && apt-get upgrade && apt-get install -y r-base-core r-base-dev \ adduser zlib1g-dev python-virtualenv python-pip libfreetype6-dev bedtools wget curl \ libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev samtools liblzma-dev \ libpcre3-dev libbz2-dev RUN pip install numpy pysam tornado matplotlib pycurl pip pandas ipython rpy2 #RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq", "DESeq2", "edgeR", "EDASeq")' #RUN Rscript -e 'install.packages(c("latticeExtra", "ggplot2", "reshape", "gridExtra"), dependencies=TRUE, repos="http://cran.us.r-project.org")' 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