diff Dockerfile @ 0:7e0392d4531c

Initial Commit.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile	Tue Dec 02 15:14:12 2014 +0100
@@ -0,0 +1,81 @@
+# Toolfactory image
+#
+# VERSION       0.1
+
+FROM debian:jessie
+
+MAINTAINER Marius van den Beek, [e-mail]
+
+# make sure the package repository is up to date
+RUN DEBIAN_FRONTEND=noninteractive apt-get -qq update
+
+# Install all requirements that are recommend by the Galaxy project
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y autoconf
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y automake
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y build-essential
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y gfortran
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y cmake
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y git-core
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libatlas-base-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libblas-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y liblapack-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y mercurial
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y subversion
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y pkg-config
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y openjdk-7-jre
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-setuptools
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y adduser
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y python-virtualenv
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y zlib1g-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libfreetype6-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y ghostscript
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y r-base-core
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y imagemagick
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y graphicsmagick-imagemagick-compat
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y exonerate
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y bedtools
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y wget
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y curl
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libcurl4-openssl-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libssl-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libreadline-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libxml2-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y samtools
+
+RUN DEBIAN_FRONTEND=noninteractive easy_install numpy
+RUN DEBIAN_FRONTEND=noninteractive easy_install pysam
+RUN DEBIAN_FRONTEND=noninteractive easy_install tornado
+RUN DEBIAN_FRONTEND=noninteractive easy_install matplotlib
+RUN DEBIAN_FRONTEND=noninteractive easy_install pycurl
+RUN DEBIAN_FRONTEND=noninteractive easy_install pip
+RUN DEBIAN_FRONTEND=noninteractive pip install metaseq
+RUN DEBIAN_FRONTEND=noninteractive easy_install pandas
+RUN DEBIAN_FRONTEND=noninteractive pip install ipython
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y zlib1g-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y liblzma-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libpcre3-dev
+RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libbz2-dev
+RUN DEBIAN_FRONTEND=noninteractive pip install rpy2
+
+RUN Rscript -e 'install.packages("latticeExtra", dependencies=TRUE, repos="http://cran.us.r-project.org")'
+RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq2")'
+RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq")'
+RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("edgeR")'
+RUN Rscript -e 'install.packages("ggplot2", dependencies=TRUE, repos="http://cran.us.r-project.org")'
+RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("EDASeq")'
+RUN Rscript -e 'install.packages("reshape", dependencies=TRUE, repos="http://cran.us.r-project.org")'
+RUN Rscript -e 'install.packages("gridExtra", dependencies=TRUE, repos="http://cran.us.r-project.org")'
+
+
+RUN adduser galaxy -u 1002
+
+#VOLUME ["/home/galaxy/"]
+#RUN chown -R galaxy /home/galaxy/ ##Doesn't work on volumes
+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