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Dockerfile
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# Dockerfile for lncRNA-Annotation-nf
# Based on debian
############################################################
# Set the base image to Ubuntu
FROM debian:jessie
# File Author / Maintainer
MAINTAINER Evan Floden <[email protected]>
# Install compiler and perl stuff
RUN apt-get update && apt-get install --yes --no-install-recommends \
wget \
ed \
less \
locales \
vim-tiny \
git \
cmake \
build-essential \
gcc-multilib \
apt-utils \
perl \
python \
ruby \
expat \
libexpat-dev \
libarchive-zip-perl \
libdbd-mysql \
libdbd-mysql-perl \
libdbd-pgsql \
libgd-gd2-perl \
libgd2-noxpm-dev \
libpixman-1-0 \
libpixman-1-dev \
graphviz \
libxml-parser-perl \
libsoap-lite-perl \
libxml-libxml-perl \
libxml-dom-xpath-perl \
libxml-libxml-simple-perl \
libxml-dom-perl \
cpanminus \
&& rm -rf /var/lib/apt/lists/*
# Install perl modules
RUN cpanm --force CPAN::Meta \
XML::Parser \
readline \
Term::ReadKey \
YAML \
Digest::SHA \
Module::Build \
ExtUtils::MakeMaker \
Test::More \
Data::Stag \
Config::Simple \
Statistics::Lite \
Statistics::Descriptive \
Parallel::ForkManager \
GD \
GD::Graph \
GD::Graph::smoothlines \
Test::Most \
Algorithm::Munkres \
Array::Compare Clone \
PostScript::TextBlock \
SVG \
SVG::Graph \
Set::Scalar \
Sort::Naturally \
Graph \
GraphViz \
HTML::TableExtract \
Convert::Binary::C \
Math::Random \
Error \
Spreadsheet::ParseExcel \
XML::Parser::PerlSAX \
XML::SAX::Writer \
XML::Twig XML::Writer \
&& rm -rf /root/.cpanm/work
# Install BioPerl last built and Guidance v2.01
RUN cpanm -v \
CJFIELDS/BioPerl-1.6.924.tar.gz \
&& apt-get update -y --fix-missing && apt-get install -y gengetopt \
libpng-dev \
time \
&& rm -rf /root/.cpanm/work \
&& wget -q -O- http://guidance.tau.ac.il/ver2/guidance.v2.01.tar.gz | tar xz && cd guidance.v2.01 && make
ENV PERL5LIB="/guidance.v2.01/www/Selecton:/guidance.v2.01/www/bioSequence_scripts_and_constants:/guidance.v2.01/www/Guidance"
#
# Clustal2
#
RUN wget -q http://www.clustal.org/download/current/clustalw-2.1-linux-x86_64-libcppstatic.tar.gz -O- \
| tar xz \
&& mv clustalw-*/clustalw2 /usr/local/bin \
&& rm -rf clustalw-*
#
# Prank
#
RUN wget -O- -q http://wasabiapp.org/download/prank/prank.source.150803.tgz | tar xz \
&& cd prank-msa/src/ \
&& make \
&& cp prank /usr/local/bin \
&& rm -rf /prank-msa
#
# Algorithm::Cluster
#
RUN cpanm -n Algorithm::Cluster
#
# FastTree
#
RUN wget -q http://www.microbesonline.org/fasttree/FastTree \
&& chmod +x FastTree \
&& cp ./FastTree /usr/local/bin/
#
# HH-Suite
#
RUN wget http://wwwuser.gwdg.de/~compbiol/data/hhsuite/releases/hhsuite-latest.tar.gz -qO- | tar xz \
&& cd hhsuite-* \
&& make && make install
ENV PATH=$PATH:/hhsuite-2.0.16/bin:/hhsuite-2.0.16/scripts
ENV HHLIB="/hhsuite-2.0.16"
ENV USER=root
#
# Download T-Coffee pre-built package
#
RUN wget -q http://www.tcoffee.org/Packages/Stable/Version_11.00.8cbe486/linux/T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz && \
tar xf T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz && \
mv T-COFFEE_installer_Version_11.00.8cbe486_linux_x64 /opt/tcoffee && \
rm -rf T-COFFEE_installer_Version_11.00.8cbe486_linux_x64.tar.gz
ENV PATH=$PATH:/opt/tcoffee/bin:/opt/tcoffee/plugins/linux/ TEMP=/tmp DIR_4_TCOFFEE=/opt/tcoffee [email protected] CACHE_4_TCOFFEE=/tmp/cache/ LOCKDIR_4_TCOFFEE=/tmp/lck/ TMP_4_TCOFFEE=/tmp/tmp/
#
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 $HOME && \
rm -rf mafft-7.130-with-extensions
#
# HMMER for esl-suite of tools
#
RUN wget -q http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2-linux-intel-x86_64.tar.gz && \
tar xf hmmer-3.1b2-linux-intel-x86_64.tar.gz
ENV PATH=$PATH:/hmmer-3.1b2-linux-intel-x86_64/binaries