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FROM ubuntu:latest
MAINTAINER Florian Heigwer "f.heigwer@dkfz.de"
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update \
&& apt-get install -y \
curl \
expat \
gcc \
git \
graphviz-dev \
g++ \
libcgi-fast-perl \
libdb-dev \
libgd-dev \
libperl-dev \
libxml2-dev \
libxt-dev \
make \
ncbi-blast+ \
openbox \
perl \
perl-debug \
perl-doc \
perl-modules \
perl-tk \
pv \
python3 \
rsync \
sudo \
wget \
xauth \
xorg \
xserver-xorg \
zlib1g-dev \
ca-certificates \
ffmpeg \
gnupg \
hicolor-icon-theme \
libglapi-mesa \
libosmesa6 \
libtbb-dev \
unzip
ENV PERL_MM_USE_DEFAULT=1
RUN perl -MCPAN -e 'CPAN::Shell->install("Bundle::CPAN")'
RUN perl -MCPAN -e 'CPAN::Shell->install("FCGI")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Bio::Perl")'
# now install all the modules we need for crispr reannotator
RUN perl -MCPAN -e 'CPAN::Shell->install("Bio::DB::Fasta")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Bio::SeqIO")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Bio::Tools::GFF")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Scalar::Util")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Term::ProgressBar")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Bio::SeqFeature::Generic")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Bio::Location::Split")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Bio::Graphics")'
RUN perl -MCPAN -e 'CPAN::Shell->install("JSON::XS")'
RUN perl -MCPAN -e 'CPAN::Shell->install("File::Slurp")'
RUN perl -MCPAN -e 'CPAN::Shell->install("List::MoreUtils")'
RUN perl -MCPAN -e 'CPAN::Shell->install("List::Util")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Archive::Zip")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Parallel::ForkManager")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Cwd")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Getopt::Long")'
RUN perl -MCPAN -e 'CPAN::Shell->install("File::Grep")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Text::Wrap")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Unix::Processors")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Spreadsheet::WriteExcel")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Text::CSV::Simple")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk")'
RUN perl -MCPAN -e 'CPAN::Shell->install("IPC::Cmd")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Getopt::Long")'
RUN perl -MCPAN -e 'CPAN::Shell->install("File::Grep")'
RUN perl -MCPAN -e 'CPAN::Shell->install("File::Spec")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Text::Wrap")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Unix::Processors")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::PathEntry")' #loads the interactive pathentry widget
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Dialog")' #loads the Tk Fileopener dialog widget
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Dressing")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::BrowseEntry")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Optionmenu")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Widget")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Frame")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Entry")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Label")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Button")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Scrollbar")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Checkbutton")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::MainWindow")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::NoteBook")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Tk::Text::SuperText")'
RUN perl -MCPAN -e 'CPAN::Shell->install("Timer::Runtime")'
ENV BOWTIE2_VERSION 2.4.5
ENV BOWTIE_VERSION 1.3.1
# Install BowTie and BowTie2
RUN wget https://downloads.sourceforge.net/project/bowtie-bio/bowtie2/$BOWTIE2_VERSION/bowtie2-$BOWTIE2_VERSION-linux-x86_64.zip \
&& unzip -d /usr/bin bowtie2-$BOWTIE2_VERSION-linux-x86_64.zip
RUN wget https://downloads.sourceforge.net/project/bowtie-bio/bowtie/$BOWTIE_VERSION/bowtie-$BOWTIE_VERSION-linux-x86_64.zip \
&& unzip -d /usr/bin bowtie-$BOWTIE_VERSION-linux-x86_64.zip \
&& chmod -R a+rwx /usr/bin/bowtie* \
&& mv /usr/bin/bowtie2*/* /usr/bin/ \
&& mv /usr/bin/bowtie*/bowtie* /usr/bin/
COPY etc/cld /var/www/cld
RUN cp /var/www/cld/cld* /usr/bin/
RUN cd /var/www/cld/depends/Set-IntervalTree-0.10-OD; perl Makefile.PL; make; make test && make install
WORKDIR /var/www
ENV LANG en-US
ENV LANGUAGE="en_US.UTF-8"
ENV LC_ALL="C"
COPY local.conf /etc/fonts/local.conf
RUN chmod -R a+rwx /usr/bin/cld*