--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile	Sat Oct 03 08:34:39 2015 -0400
@@ -0,0 +1,38 @@
+# 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