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Dockerfile
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FROM pditommaso/dkrbase:1.2
MAINTAINER Paolo Di Tommaso <[email protected]>
#
# Add Python setup tools
#
RUN apt-get update --fix-missing && apt-get install -y python-setuptools
#
# BLAST
#
RUN wget -q ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.29/ncbi-blast-2.2.29+-x64-linux.tar.gz -O- \
| tar xz -C /opt && \
ln -s /opt/ncbi-blast-2.2.29+/ /opt/blast;
#
# MAFFT
#
RUN wget -q http://mafft.cbrc.jp/alignment/software/mafft-7.130-with-extensions-src.tgz -O- \
| tar xz && \
cd mafft-7.130-with-extensions/core && \
make && make install && \
cd $HOME && \
rm -rf mafft-7.130-with-extensions
#
# SATe
#
RUN easy_install -U dendropy && \
cd /opt && \
wget -q http://phylo.bio.ku.edu/software/sate/downloads2/src/satesrc-v2.2.7-2013Feb15.tar.gz -O- \
| tar xz && \
cd satesrc-v2.2.7-2013Feb15/sate-core/ && \
python setup.py develop && \
cd /opt && \
ln -s /opt/satesrc-v2.2.7-2013Feb15 /opt/sate
#
# CLUSTALO
#
RUN wget -q http://www.clustal.org/omega/clustalo-1.2.0-Ubuntu-x86_64 && \
chmod +x clustalo-1.2.0-Ubuntu-x86_64 && \
mv clustalo-1.2.0-Ubuntu-x86_64 /usr/local/bin/clustalo
#
# T-COffee
#
RUN wget -q http://www.tcoffee.org/Packages/Beta/Version_10.00.04ad7ba/linux/T-COFFEE_installer_Version_10.00.04ad7ba_linux_x64.tar.gz -O- \
| tar xz && \
mv T-COFFEE_installer_Version_10.00.04ad7ba_linux_x64 /opt/tcoffee
#
# Perl modules required by T-Coffee
#
RUN cpanm -q -n Env Net::SSLeay XML::Simple SOAP::Lite && \
rm -rf /root/.cpanm/work/
#
# SETUP the environment
#
ENV SATE_HOME /opt/sate/
ENV PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/blast/bin:/opt/sate/sate-core/bin:/opt/tcoffee/bin:/opt/tcoffee/plugins/linux/
ENV TEMP /tmp
ENV DIR_4_TCOFFEE /opt/tcoffee
ENV EMAIL_4_TCOFFEE [email protected]
ENV CACHE_4_TCOFFEE /tmp/cache/
ENV LOCKDIR_4_TCOFFEE /tmp/lck/
ENV TMP_4_TCOFFEE /tmp/tmp/