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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 usermod -U www-data && chsh -s /bin/bash www-data
COPY enable-var-www-html-htaccess.conf /etc/apache2/conf-enabled/
COPY run_apache.sh /var/www/
RUN a2enmod rewrite cgi perl headers
volume "/var/log"
#USER www-data
#VOLUME ["/var/www/html", "/var/log/apache2" ]
ENV SERVER_NAME docker-apache-php
# for main web interface:
EXPOSE 80
WORKDIR /var/www/html
## Installing perl module
RUN apt-get install make && curl -L http://cpanmin.us | perl - App::cpanminus
RUN cpanm SVG
###____________________________________________
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 GBlocks
RUN curl -SL http://molevol.cmima.csic.es/castresana/Gblocks/Gblocks_Linux64_0.91b.tar.Z | tar -xzC /opt && ln -s /opt/Gblocks_0.91b/Gblocks /usr/bin/Gblocks
####___________________________________________________________________________________________________________________________________
RUN apt-get install -y build-essential
## Instaling Quicktree
RUN wget -O /opt/quicktree.tar.gz ftp://ftp.sanger.ac.uk/pub/resources/software/quicktree/quicktree.tar.gz
RUN mkdir /opt/quicktree && tar -C /opt/quicktree -zxvf /opt/quicktree.tar.gz && cd /opt/quicktree/quicktree_1.1 && make quicktree
#___________________________________________________________________________________________________________________________________
# 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
#_________________________________________________________________________________________________
## CORASON
# RUN git clone https://github.com/nselem/EvoDivMet
# RUN mkdir /opt/CORASON
######### PATHS ENVIRONMENT
ENV PATH /opt/blast/bin:$PATH:/opt/muscle:/opt/Gblocks:/opt/quicktree/quicktree_1.1/bin:/root/EvoDivMet/CORASON
## Moving to myapp directory
# RUN mkdir /usr/src/CORASON
### Aqui puedo pasar GENOMES, query, RAST_IDs
# COPY . /usr/src/CORASON
CMD ["/var/www/run_apache.sh"]