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planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
author mvdbeek
date Sat, 03 Oct 2015 08:59:09 -0400
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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1 # Toolfactory image
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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2 #
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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3 # VERSION 0.2
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4 # This Dockerfile is the base system for executing scripts by the DockerToolFactory.
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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6 FROM toolshed/requirements
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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8 MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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10 # make sure the package repository is up to date
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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11 ENV DEBIAN_FRONTEND noninteractive
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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13 #add galaxy user (could be any username).
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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14 #1001 will be replaced by the actual user id of the system user
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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15 #executing the galaxy tool, so that file write operations are possible.
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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16 RUN adduser galaxy -u 1000
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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19 ADD adduser.sh /usr/local/bin/adduser.sh
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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20 RUN adduser.sh
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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22 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 \
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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23 "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 \
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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24 adduser zlib1g-dev python-virtualenv python-pip libfreetype6-dev bedtools wget curl \
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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25 libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev samtools liblzma-dev \
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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26 libpcre3-dev libbz2-dev
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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28 RUN pip install numpy pysam tornado matplotlib pycurl pip pandas ipython rpy2
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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30 #RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq", "DESeq2", "edgeR", "EDASeq")'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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31 #RUN Rscript -e 'install.packages(c("latticeExtra", "ggplot2", "reshape", "gridExtra"), dependencies=TRUE, repos="http://cran.us.r-project.org")'
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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33 RUN mkdir /home/galaxy/job_working_directory
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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34 WORKDIR /home/galaxy/job_working_directory
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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35 USER galaxy
0fa46413d0d9 planemo upload for repository https://bitbucket.org/mvdbeek/dockertoolfactory/ commit 2f33eb59c06ac3d6ba6e22622fd4ae729eb5e4da-dirty
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37 #ENTRYPOINT chown -R galaxy /home/galaxy/ && su - galaxy
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38 CMD /bin/bash