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Dockerfile
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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 <evanfloden@gmail.com>
# 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 \
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
RUN cpanm -v \
CJFIELDS/BioPerl-1.6.924.tar.gz \
&& rm -rf /root/.cpanm/work
# Install R
RUN echo "deb http://cran.rstudio.com/bin/linux/debian jessie-cran3/" >> /etc/apt/sources.list \
&& apt-key adv --keyserver keys.gnupg.net --recv-key 381BA480 \
&& apt-get update --fix-missing \
&& apt-get -y install r-base
# Install R libraries
RUN R -e 'install.packages("ROCR", repos="http://cloud.r-project.org/"); install.packages("randomForest",repos="http://cloud.r-project.org/")'
# Install Star Mapper
RUN wget -qO- https://github.com/alexdobin/STAR/archive/2.5.2a.tar.gz | tar -xz \
&& cd STAR-2.5.2a \
&& make STAR
# Install FEELnc
RUN wget -q https://github.com/tderrien/FEELnc/archive/a6146996e06f8a206a0ae6fd59f8ca635c7d9467.zip \
&& unzip a6146996e06f8a206a0ae6fd59f8ca635c7d9467.zip \
&& mv FEELnc-a6146996e06f8a206a0ae6fd59f8ca635c7d9467 /FEELnc \
&& rm a6146996e06f8a206a0ae6fd59f8ca635c7d9467.zip
ENV FEELNCPATH /FEELnc
ENV PERL5LIB $PERL5LIB:${FEELNCPATH}/lib/
# Install Cufflinks/Cuffmerge
RUN wget -qO- http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz | tar xz
ENV PATH $PATH:/FEELnc/bin/LINUX:/FEELnc/utils:/FEELnc/scripts/:/cufflinks-2.2.1.Linux_x86_64:/STAR-2.5.2a/bin/Linux_x86_64/