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‎README.md

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Dockerfiles
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===========
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This repository contains Dockerfile used to make Docker images used at Genomic Paris Centre.

‎bcl2fastq/bcl2fastq-1.8.4/Dockerfile

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############################################################
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# Dockerfile to build bcl2fastq container images
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# Based on CentOS images made by fatherlinux
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# fatherlinux is a RedHat developer
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# http://developerblog.redhat.com/2014/05/15/practical-introduction-to-docker-containers/
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############################################################
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# Set the base image to CentOS 5
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FROM fatherlinux/centos5-base:latest
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Download Bcl2FastQ
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RUN cd /tmp ; wget ftp://webdata:webdata@ussd-ftp.illumina.com/Downloads/Software/bcl2fastq/bcl2fastq-1.8.4-Linux-x86_64.rpm
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# Install OLB dependencies
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RUN yum -y --nogpgcheck localinstall /tmp/bcl2fastq-*.rpm
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# Cleanup
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RUN rm -rf /tmp/*.rpm

‎casava/casava-1.8.2/Dockerfile

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############################################################
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# Dockerfile to build casava container images
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# Based on CentOS images made by fatherlinux
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# fatherlinux is a RedHat developer
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# http://developerblog.redhat.com/2014/05/15/practical-introduction-to-docker-containers/
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############################################################
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# Set the base image to CentOS 5
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FROM fatherlinux/centos5-base:latest
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Install OLB dependencies
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RUN yum -y install make perl python PyXML gnuplot ImageMagick ghostscript libxslt libxslt-devel libxml2 libxml2-devel libxml2-python ncurses ncurses-devel gcc gcc-c++ libtiff libtiff-devel bzip2 bzip2-devel zlib zlib-devel perl-XML-Dumper perl-XML-Grove perl-XML-LibXML perl-XML-LibXML-Common perl-XML-NamespaceSupport perl-XML-Parser perl-XML-SAX perl-XML-Simple perl-XML-Twig perldoc
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# Download CASAVA
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ADD http://supportres.illumina.com/documents/myillumina/6e422abb-dc36-4d09-b223-0eafef26ddc5/casava_v1.8.2.tar /tmp/
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# Uncompress CASAVA archive
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RUN tar -C /tmp -xjf /tmp/casava*.tar
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# Install CASAVA
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RUN ln -s /tmp/CASAVA_* /tmp/CASAVA
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RUN mkdir /tmp/CASAVA-build && cd /tmp/CASAVA-build && /tmp/CASAVA/src/configure --prefix=/usr/local && make && make install
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# Cleanup
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RUN rm -rf /tmp/casava* /tmp/CASAVA*

‎deseq/deseq-1.8.3/Dockerfile

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############################################################
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# Dockerfile to build DESeq container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM ubuntu:12.04
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren
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# Add CRAN source to apt
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RUN echo "deb http://cran.r-project.org/bin/linux/ubuntu precise/" > /etc/apt/sources.list.d/cran.list
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# Add CRAN apt key
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RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
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# Update the repository sources list
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RUN apt-get update
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# Install Latex
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RUN apt-get install --yes texlive-latex-base texlive-latex-extra
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# Install libxml2
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RUN apt-get install --yes libxml2-dev
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# Install R 2.15
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RUN apt-get install --yes r-base=2.15.0-1precise0 r-base-core=2.15.0-1precise0 r-base-dev=2.15.0-1precise0 r-base-html=2.15.0-1precise0 r-recommended=2.15.0-1precise0 r-base=2.15.0-1precise0 r-base-core=2.15.0-1precise0 r-base-dev=2.15.0-1precise0 r-base-html=2.15.0-1precise0 r-cran-boot=1.3-4-1precise0 r-cran-class=7.3-3-1precise0 r-cran-cluster=1.14.2-1precise0 r-cran-codetools=0.2-8-1precise0 r-cran-foreign=0.8.50-1precise0 r-cran-kernsmooth=2.23-7-1precise0 r-cran-lattice=0.20-6-1precise0 r-cran-mass=7.3-18-1precise0 r-cran-matrix=1.0-6-1precise0 r-cran-mgcv=1.7-17-1precise0 r-cran-rpart=3.1.52-1precise0 r-doc-html=2.15.0-1precise0 r-recommended=2.15.0-1precise0 r-cran-nlme=3.1.104-1precise0 r-cran-survival=2.36-14-1precise0 r-cran-nnet=7.3-1-2precise0 r-cran-spatial=7.3-3-1precise0
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# Set CRAN repository to use
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RUN echo 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)})' > ~/.Rprofile
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# Install bioconductor
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RUN R -e 'install.packages("XML"); source("http://bioconductor.org/biocLite.R"); biocLite("DESeq") ; install.packages("FactoMineR")'
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# Cleanup
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RUN apt-get clean
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# Default command to execute at startup of the container
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CMD R --no-save

‎deseq/deseq2-1.4.4/Dockerfile

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############################################################
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# Dockerfile to build DESeq container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM ubuntu:12.04
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren
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# Add CRAN source to apt
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RUN echo "deb http://cran.r-project.org/bin/linux/ubuntu precise/" > /etc/apt/sources.list.d/cran.list
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# Add CRAN apt key
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RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
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# Update the repository sources list
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RUN apt-get update
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# Install Latex
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RUN apt-get install --yes texlive-latex-base texlive-latex-extra
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# Install libxml2
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RUN apt-get install --yes libxml2-dev
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# Install R 3.1.0
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RUN apt-get install --yes r-base=3.1.0-1precise0 r-base-core=3.1.0-1precise0 r-base-dev=3.1.0-1precise0 r-base-html=3.1.0-1precise0 r-doc-html=3.1.0-1precise0 r-recommended=3.1.0-1precise0 r-cran-boot=1.3-11-1precise0 r-cran-class=7.3-10-1precise0 r-cran-cluster=1.15.2-1precise0 r-cran-codetools=0.2-8-2precise0 r-cran-foreign=0.8.61-1precise0 r-cran-kernsmooth=2.23-12-1precise0 r-cran-lattice=0.20-29-1precise0 r-cran-mass=7.3-33-1precise0 r-cran-matrix=1.1-3-1precise0 r-cran-mgcv=1.7-29-1precise0 r-cran-nlme=3.1.117-1precise0 r-cran-nnet=7.3-8-1precise0 r-cran-rpart=4.1-8-1precise0 r-cran-spatial=7.3-6-1precise0 r-cran-survival=2.37-7-1precise0
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# Set CRAN repository to use
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RUN echo 'local({r <- getOption("repos"); r["CRAN"] <- "http://cran.r-project.org"; options(repos=r)})' > ~/.Rprofile
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# Install bioconductor
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RUN R -e 'source("http://bioconductor.org/biocLite.R"); biocLite("DESeq2")'
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# Cleanup
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RUN apt-get clean
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# Default command to execute at startup of the container
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CMD R --no-save

‎eoulsan/eoulsan-1.2.2/Dockerfile

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############################################################
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# Dockerfile to build Eoulsan container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM genomicpariscentre/deseq:latest
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Update the repository sources list
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RUN apt-get update
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# Install OpenJDK 7 JRE
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RUN apt-get install --yes openjdk-7-jre-headless
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# Download and install Eoulsan
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ADD http://www.transcriptome.ens.fr/eoulsan/eoulsan-1.2.2.tar.gz /tmp/
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# Install Eoulsan
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RUN ls /tmp/eoulsan-*.tar.gz
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RUN tar --directory /usr/local -xf /tmp/eoulsan-*.tar.gz
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# Create links for eoulsan.sh to get eoulsan.sh in PATH
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RUN ln -s /usr/local/eoulsan-*/eoulsan.sh /usr/local/bin/eoulsan.sh
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RUN ln -s /usr/local/eoulsan-*/eoulsan.sh /usr/local/bin/eoulsan
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# Patch bug in eoulsan.sh
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RUN cat /usr/local/eoulsan-*/eoulsan.sh | sed 's/BASEDIR=`dirname $0`/ARG0=`readlink $0` ; BASEDIR=`dirname $ARG0`/' > /tmp/eoulsan.sh && mv /tmp/eoulsan.sh /usr/local/eoulsan-*/eoulsan.sh && chmod +x /usr/local/eoulsan-*/eoulsan.sh
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# Cleanup
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RUN rm -rf /tmp/eoulsan-*.tar.gz
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RUN apt-get clean
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# Default command to execute at startup of the container
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CMD eoulsan.sh --version

‎fastqc/fastqc-0.10.0/Dockerfile

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############################################################
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# Dockerfile to build FASTQC container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM ubuntu:12.04
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Update the repository sources list
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RUN apt-get update
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# Install OpenJDK 7 JRE
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RUN apt-get install --yes openjdk-7-jre-headless perl unzip
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# Download FastQC
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ADD http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.0.zip /tmp/
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# Install FastQC
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RUN cd /usr/local ; unzip /tmp/fastqc_*.zip
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RUN chmod 755 /usr/local/FastQC/fastqc
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RUN ln -s /usr/local/FastQC/fastqc /usr/local/bin/fastqc
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# Cleanup
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RUN rm -rf /tmp/fastqc_*.zip

‎fastqc/fastqc-0.10.1/Dockerfile

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############################################################
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# Dockerfile to build FASTQC container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM ubuntu:12.04
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Update the repository sources list
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RUN apt-get update
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# Install OpenJDK 7 JRE
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RUN apt-get install --yes openjdk-7-jre-headless perl unzip
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# Download FastQC
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ADD http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.10.1.zip /tmp/
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# Install FastQC
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RUN cd /usr/local ; unzip /tmp/fastqc_*.zip
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RUN chmod 755 /usr/local/FastQC/fastqc
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RUN ln -s /usr/local/FastQC/fastqc /usr/local/bin/fastqc
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# Cleanup
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RUN rm -rf /tmp/fastqc_*.zip

‎fastqc/fastqc-0.11.1/Dockerfile

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############################################################
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# Dockerfile to build FASTQC container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM ubuntu:12.04
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Update the repository sources list
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RUN apt-get update
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# Install OpenJDK 7 JRE
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RUN apt-get install --yes openjdk-7-jre-headless perl unzip
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# Download FastQC
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ADD http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.1.zip /tmp/
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# Install FastQC
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RUN cd /usr/local ; unzip /tmp/fastqc_*.zip
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RUN chmod 755 /usr/local/FastQC/fastqc
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RUN ln -s /usr/local/FastQC/fastqc /usr/local/bin/fastqc
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# Cleanup
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RUN rm -rf /tmp/fastqc_*.zip

‎fastqc/fastqc-0.11.2/Dockerfile

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############################################################
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# Dockerfile to build FASTQC container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM ubuntu:12.04
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Update the repository sources list
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RUN apt-get update
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# Install OpenJDK 7 JRE
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RUN apt-get install --yes openjdk-7-jre-headless perl unzip
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# Download FastQC
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ADD http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.2.zip /tmp/
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# Install FastQC
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RUN cd /usr/local ; unzip /tmp/fastqc_*.zip
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RUN chmod 755 /usr/local/FastQC/fastqc
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RUN ln -s /usr/local/FastQC/fastqc /usr/local/bin/fastqc
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# Cleanup
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RUN rm -rf /tmp/fastqc_*.zip

‎htseq/htseq-0.5.3p9/Dockerfile

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############################################################
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# Dockerfile to build HTSeq container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM ubuntu:12.04
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Update the repository sources list
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RUN apt-get update
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# Install Latex
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RUN apt-get install --yes build-essential python2.7-dev python-numpy python-matplotlib
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# Download and uncompress HTSeq archive
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ADD HTSeq-0.5.3p9.tar.gz /tmp/
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# Install HTSeq
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RUN cd /tmp/* && python setup.py build && python setup.py install
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# Cleanup
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RUN apt-get clean
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RUN rm -rf /tmp/*

‎htseq/htseq-0.5.3p9/HTSeq-0.5.3p9.tar.gz

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‎htseq/htseq-0.5.4p1/Dockerfile

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############################################################
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# Dockerfile to build HTSeq container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM ubuntu:12.04
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Update the repository sources list
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RUN apt-get update
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# Install Latex
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RUN apt-get install --yes build-essential python2.7-dev python-numpy python-matplotlib
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# Download and uncompress HTSeq archive
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ADD HTSeq-0.5.4p1.tar.gz /tmp/
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# Install HTSeq
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RUN cd /tmp/* && python setup.py build && python setup.py install
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# Cleanup
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RUN apt-get clean
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RUN rm -rf /tmp/*

‎htseq/htseq-0.5.4p1/HTSeq-0.5.4p1.tar.gz

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‎htseq/htseq-0.6.1p1/Dockerfile

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############################################################
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# Dockerfile to build HTSeq container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM ubuntu:12.04
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Update the repository sources list
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RUN apt-get update
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# Install Latex
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RUN apt-get install --yes build-essential python2.7-dev python-numpy python-matplotlib
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# Download and uncompress HTSeq archive
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ADD HTSeq-0.6.1p1.tar.gz /tmp/
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# Install HTSeq
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RUN cd /tmp/* && python setup.py build && python setup.py install
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# Cleanup
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RUN apt-get clean
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RUN rm -rf /tmp/*

‎htseq/htseq-0.6.1p1/HTSeq-0.6.1p1.tar.gz

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‎macs/macs-1.4.2/Dockerfile

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############################################################
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# Dockerfile to build MACS container images
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# Based on Ubuntu
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############################################################
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# Set the base image to Ubuntu
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FROM ubuntu:12.04
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# File Author / Maintainer
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MAINTAINER Laurent Jourdren <jourdren@biologie.ens.fr>
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# Update the repository sources list
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RUN apt-get update
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# Install Latex
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RUN apt-get install --yes python
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# Download MACS
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ADD https://github.com/downloads/taoliu/MACS/macs_1.4.2_python2.7.deb /tmp/
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# Install MACS
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RUN dpkg -i /tmp/*.deb
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# Cleanup
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RUN apt-get clean
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RUN rm /tmp/*.deb
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# Default command to execute at startup of the container
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CMD macs14

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