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Dockerfile
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FROM ubuntu:14.04
MAINTAINER Jindrich Vimr <[email protected]>
RUN echo "1.565.1" > .lts-version-number
RUN apt-get update && apt-get install -y wget git curl zip vim
RUN apt-get update && apt-get install -y apache2 php5 perl libapache2-mod-perl2 php5-mysql libdbd-mysql-perl libdatetime-format-builder-perl libemail-abstract-perl libemail-send-perl libemail-simple-perl libemail-mime-perl libtemplate-perl libmath-random-isaac-perl libgd-text-perl libgd-graph-perl libxml-twig-perl libchart-perl libnet-ldapapi-perl libtemplate-plugin-gd-perl libfile-slurp-perl libhtml-scrubber-perl libhtml-formattext-withlinks-perl libjson-rpc-perl libjson-xs-perl libnet-ldap-perl libauthen-radius-perl libencode-detect-perl libfile-mimeinfo-perl libio-stringy-perl libdaemon-generic-perl
RUN apt-get update && apt-get install -y php5-intl imagemagick
RUN apt-get install -y build-essential
RUN usermod -U www-data && chsh -s /bin/bash www-data
RUN a2enmod rewrite cgi perl headers
volume "/var/log"
# for main web interface:
ENV SERVER_NAME docker-apache-php
EXPOSE 80
####___________________________________________________________________________________________________________________________________
## Installing perl modules
RUN apt-get install make && curl -L http://cpanmin.us | perl - App::cpanminus
RUN cpanm SVG
RUN cpanm Statistics::Basic
RUN cpanm IO::Tee
RUN cpanm Bio::SeqIO
###____________________________________________
RUN if [ ! -d /opt ]; then mkdir /opt; fi
###__________________________________________________________________________________________________________________________________
# Installing blast
RUN mkdir /opt/blast && curl ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-x64-linux.tar.gz | tar -zxC /opt/blast --strip-components=1
######___________________________________________________________________________________________________________________________________
# Instaling muscle
RUN wget -O /opt/muscle3.8.tar.gz http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
RUN mkdir /opt/muscle && tar -C /opt/muscle -xzvf /opt/muscle3.8.tar.gz && ln -s /opt/muscle/muscle3.8.31_i86linux64 /opt/muscle/muscle
####___________________________________________________________________________________________________________________________________
# Installing NewickTools
RUN wget -O /opt/newick-utils-1.6.tar.gz http://cegg.unige.ch/pub/newick-utils-1.6-Linux-x86_64-disabled-extra.tar.gz
RUN mkdir /opt/nw && tar -C /opt/nw -xzvf /opt/newick-utils-1.6.tar.gz && cd /opt/nw/newick-utils-1.6 && cp src/nw_* /usr/local/bin
#_________________________________________________________________________________________________
## Instaling FastTree
RUN mkdir /opt/fasttree && wget -O /opt/fasttree/FastTree http://www.microbesonline.org/fasttree/FastTree && chmod +x /opt/fasttree/FastTree
#--------------------------------------------------------------------
WORKDIR /var/www/
#RUN mkdir /var/www/html
RUN chmod -R 777 /var/www/html
## EvoMining
RUN git clone https://github.com/nselem/EvoMining /var/www/html/EvoMining
#--------------------------------------------------------------------
# Installing GBlocks
RUN zcat /var/www/html/EvoMining/cgi-bin/Gblocks_Linux64_0.91b.tar.Z | tar -xvf -
#----------------------------------------------------------------------------------
RUN mv /var/www/html/EvoMining/enable-var-www-html-htaccess.conf /etc/apache2/conf-enabled/
RUN mv /var/www/html/EvoMining/apache2.conf /etc/apache2/
RUN service apache2 start
RUN chmod -R 777 /var/www/html/EvoMining
######### PATHS ENVIRONMENT
ENV PATH /opt/blast/bin:$PATH:/opt/muscle:/opt/quicktree/quicktree_1.1/bin:/opt/fasttree:/var/www/html/EvoMining/cgi-bin
RUN chmod +x /var/www/html/EvoMining/cgi-bin/*pl
WORKDIR /var/www/html/EvoMining/cgi-bin
CMD ["perl", "startEvoMining.pl"]