comparison Dockerfile @ 2:5b930e77b1f3

Better readability of Dockerfile, fix editing of userid for Dockerfile in DockerToolFactory.py.

1:5d70248d1e01

# 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

2:5b930e77b1f3

# 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, [e-mail]

# 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("DESeq", "DESeq2", "edgeR", "EDASeq")'
RUN Rscript -e 'install.packages(c("latticeExtra", "ggplot2", "reshape", "gridExtra"), dependencies=TRUE, repos="http://cran.us.r-project.org")'

#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 1001

#VOLUME ["/home/galaxy/"]
RUN mkdir /home/galaxy/job_working_directory
WORKDIR /home/galaxy/job_working_directory
USER galaxy