Mercurial > repos > mvdbeek > docker_toolfactory_alpha

comparison Dockerfile @ 2:5b930e77b1f3

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Better readability of Dockerfile, fix editing of userid for Dockerfile in DockerToolFactory.py.
author mvdbeek
date Wed, 03 Dec 2014 00:26:43 +0100
parents 7e0392d4531c
children 477eac6c4cea
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1:5d70248d1e01 2:5b930e77b1f3
1 # Toolfactory image 1 # Toolfactory image
2 # 2 #
3 # VERSION 0.1 3 # VERSION 0.1
4 # This Dockerfile is the base system for executing scripts by the DockerToolFactory.
4 5
5 FROM debian:jessie 6 FROM debian:jessie
6 7
7 MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com 8 MAINTAINER Marius van den Beek, m.vandenbeek@gmail.com
8 9
9 # make sure the package repository is up to date 10 # make sure the package repository is up to date
10 RUN DEBIAN_FRONTEND=noninteractive apt-get -qq update 11 ENV DEBIAN_FRONTEND noninteractive
12 RUN apt-get -qq update
11 13
12 # Install all requirements that are recommend by the Galaxy project 14 # Install all requirements that are recommend by the Galaxy project
13 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y autoconf 15 RUN apt-get install --no-install-recommends -y autoconf automake build-essential gfortran \
14 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y automake 16 cmake git-core libatlas-base-dev libblas-dev liblapack-dev mercurial subversion python-dev \
15 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y build-essential 17 pkg-config openjdk-7-jre python-setuptools adduser zlib1g-dev ghostscript r-base-core \
16 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y gfortran 18 graphicsmagick-imagemagick-compat
17 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y cmake
18 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y git-core
19 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libatlas-base-dev
20 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libblas-dev
21 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y liblapack-dev
22 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y mercurial
23 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y subversion
24 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-dev
25 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y pkg-config
26 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y openjdk-7-jre
27 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y python-setuptools
28 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y adduser
29 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y python-virtualenv
30 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y zlib1g-dev
31 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libfreetype6-dev
32 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y ghostscript
33 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y r-base-core
34 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y imagemagick
35 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y graphicsmagick-imagemagick-compat
36 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y exonerate
37 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y bedtools
38 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y wget
39 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y curl
40 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libcurl4-openssl-dev
41 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libssl-dev
42 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libreadline-dev
43 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y libxml2-dev
44 RUN DEBIAN_FRONTEND=noninteractive apt-get install --no-install-recommends -y samtools
45 19
46 RUN DEBIAN_FRONTEND=noninteractive easy_install numpy 20 RUN apt-get install -y python-virtualenv libfreetype6-dev exonerate bedtools wget curl \
47 RUN DEBIAN_FRONTEND=noninteractive easy_install pysam 21 libcurl4-openssl-dev libssl-dev libreadline-dev libxml2-dev samtools liblzma-dev \
48 RUN DEBIAN_FRONTEND=noninteractive easy_install tornado 22 libpcre3-dev libbz2-dev
49 RUN DEBIAN_FRONTEND=noninteractive easy_install matplotlib
50 RUN DEBIAN_FRONTEND=noninteractive easy_install pycurl
51 RUN DEBIAN_FRONTEND=noninteractive easy_install pip
52 RUN DEBIAN_FRONTEND=noninteractive pip install metaseq
53 RUN DEBIAN_FRONTEND=noninteractive easy_install pandas
54 RUN DEBIAN_FRONTEND=noninteractive pip install ipython
55 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y zlib1g-dev
56 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y liblzma-dev
57 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libpcre3-dev
58 RUN DEBIAN_FRONTEND=noninteractive apt-get install -y libbz2-dev
59 RUN DEBIAN_FRONTEND=noninteractive pip install rpy2
60 23
61 RUN Rscript -e 'install.packages("latticeExtra", dependencies=TRUE, repos="http://cran.us.r-project.org")' 24 RUN easy_install pip
62 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq2")'
63 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq")'
64 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("edgeR")'
65 RUN Rscript -e 'install.packages("ggplot2", dependencies=TRUE, repos="http://cran.us.r-project.org")'
66 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("EDASeq")'
67 RUN Rscript -e 'install.packages("reshape", dependencies=TRUE, repos="http://cran.us.r-project.org")'
68 RUN Rscript -e 'install.packages("gridExtra", dependencies=TRUE, repos="http://cran.us.r-project.org")'
69 25
26 RUN pip install numpy pysam tornado matplotlib pip pandas ipython rpy2
70 27
71 RUN adduser galaxy -u 1002 28 RUN Rscript -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq", "DESeq2", "edgeR", "EDASeq")'
29 RUN Rscript -e 'install.packages(c("latticeExtra", "ggplot2", "reshape", "gridExtra"), dependencies=TRUE, repos="http://cran.us.r-project.org")'
30
31 #add galaxy user (could be any username).
32 #1001 will be replaced by the actual user id of the system user
33 #executing the galaxy tool, so that file write operations are possible.
34 RUN adduser galaxy -u 1001
72 35
73 #VOLUME ["/home/galaxy/"] 36 #VOLUME ["/home/galaxy/"]
74 #RUN chown -R galaxy /home/galaxy/ ##Doesn't work on volumes
75 RUN mkdir /home/galaxy/job_working_directory 37 RUN mkdir /home/galaxy/job_working_directory
76 WORKDIR /home/galaxy/job_working_directory 38 WORKDIR /home/galaxy/job_working_directory
77 USER galaxy 39 USER galaxy
78 40
79 41