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Dockerfile
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FROM ubuntu:precise
MAINTAINER Paolo Di Tommaso <paolo.ditommaso@gmail.com>
#
# Install pre-requistes
#
RUN apt-get update -q --fix-missing; \
apt-get install -q -y openjdk-7-jre-headless wget curl unzip;
# Samtools + Cufflinks
RUN apt-get install -q -y samtools libboost-all-dev
# Cufflinks
RUN wget -q http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.1.1.Linux_x86_64.tar.gz; \
tar xf cufflinks-2.1.1.Linux_x86_64.tar.gz -C /opt; \
rm -rf cufflinks-2.1.1.Linux_x86_64.tar.gz; \
ln -s /opt/cufflinks-2.1.1.Linux_x86_64/ /opt/cufflinks
# GEMtools
RUN wget -q http://barnaserver.com/gemtools/releases/GEMTools-static-core2-1.7.1.tar.gz; \
tar xf GEMTools-static-core2-1.7.1.tar.gz -C /opt; \
rm -rf GEMTools-static-core2-1.7.1.tar.gz; \
ln -s /opt/gemtools-1.7.1-core2 /opt/gemtools
# Flux Capacitor
RUN wget -q http://sammeth.net/artifactory/barna/barna/barna.capacitor/1.2.4/flux-capacitor-1.2.4.tgz; \
tar xf flux-capacitor-1.2.4.tgz -C /opt; \
rm -rf flux-capacitor-1.2.4.tgz; \
ln -s /opt/flux-capacitor-1.2.4 /opt/flux
# Bowtie
RUN wget -q -O bowtie2-2.2.1-linux-x86_64.zip \
'http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.1/bowtie2-2.2.1-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie2%2F2.2.1%2F&ts=1395738113&use_mirror=freefr'; \
unzip -q bowtie2-2.2.1-linux-x86_64.zip -d /opt; \
rm -rf bowtie2-2.2.1-linux-x86_64.zip; \
ln -s /opt/bowtie2-2.2.1 /opt/bowtie2
# Install tophat2
RUN wget -q http://tophat.cbcb.umd.edu/downloads/tophat-2.0.11.Linux_x86_64.tar.gz; \
tar xf tophat-2.0.11.Linux_x86_64.tar.gz -C /opt; \
rm -rf tophat-2.0.11.Linux_x86_64.tar.gz; \
ln -s /opt/tophat-2.0.11.Linux_x86_64 /opt/tophat2
ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/cufflinks:/opt/gemtools/bin:/opt/flux/bin:/opt/bowtie2:/opt/tophat2