3. System requirements

NOTE: There is an online version of EDGE, found on https://edgebioinformatics.org/ is hosted at Texas Advanced Computing Center (TACC) with 128G memory and 44 CPUs.

The current version of the EDGE pipeline has been extensively tested on a Linux Server with Ubuntu 18.04 and CentOS 6.5/7 operating system and will work on 64bit Linux environments.

3.1. Hardware Requirements

Due to the involvement of several high memory and high cpu consuming steps Minimum requirement: 24GB memory, at least 8 computing CPUs and 1 TB disk space. A higher computer spec is strongly recommended: 256GB memory, 64 computing CPUs and > 4 TB disk space. Please ensure that your system has the essential software packages installed properly before running the installing script. The following should be installed by a system administrator (requires sudo).

Note

If your system OS is neither Ubuntu 18.04 or CentOS 7.0, it may have differnt packages/libraries name and the newer complier on newer OS may fail on compling some of thirdparty bioinformatics tools. We would suggest to use EDGE Docker container.

3.2. Ubuntu 18.04

https://assets.ubuntu.com/v1/8dd99b80-ubuntu-logo14.png

  1. Install build essential libraries and dependancies:

    sudo apt-get update

sudo apt-get install -y build-essential libreadline-gplv2-dev libx11-dev \
    libxt-dev libgsl-dev libfreetype6-dev libncurses5-dev gfortran \
    inkscape libwww-perl libxml-libxml-perl libperlio-gzip-perl  \
    zlib1g-dev zip unzip libjson-perl libpng-dev cpanminus default-jre \
    firefox wget curl csh liblapack-dev libblas-dev libatlas-base-dev \
    libcairo2-dev libssh2-1-dev libssl-dev libcurl4-openssl-dev bzip2 \
    bioperl rsync libbz2-dev liblzma-dev time libterm-readkey-perl \
    liblwp-protocol-https-perl gnuplot libjson-xs-perl libio-socket-ip-perl \
    vim php sendmail mysql-client mysql-server libgfortran3  texinfo \
    openssh-server openssh-client openjdk-11-jdk texlive git gawk \
    texlive-fonts-extra libboost-all-dev cron less libxml2-dev \
    libcgi-pm-perl libxml-simple-perl libxml-dom-perl locales \
    libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl ghostscript

  2. Install Apache2 for EDGE UI:

    sudo apt-get install apache2
sudo a2enmod cgid proxy proxy_http headers rewrite

  3. Install packages for user management system:

    sudo apt-get install sendmail mysql-client mysql-server

cd /usr/share
wget https://archive.apache.org/dist/tomcat/tomcat-7/v7.0.109/bin/apache-tomcat-7.0.109.tar.gz
tar xzf apache-tomcat-7.0.109.tar.gz
rm apache-tomcat-7.0.109.tar.gz
mv apache-tomcat-7.0.109 tomcat7
echo "export CATALINA_HOME=\"/usr/share/tomcat7\"" >> /etc/profile

  4. Change the image conversion policy:

    sed -i.bak 's/rights=\"none\" pattern=\"PDF\"/rights=\"read|write\" pattern=\"PDF\"/' /etc/ImageMagick-6/policy.xml

3.3. CentOS 7

https://upload.wikimedia.org/wikipedia/commons/thumb/b/bc/Centos_full.svg/200px-Centos_full.svg.png

  1. Install libraries and dependencies by yum:

    # add epel reporsitory
sudo yum -y install epel-release

sudo yum install -y libX11-devel readline-devel libXt-devel ncurses-devel inkscape \
    expat expat-devel freetype freetype-devel zlib zlib-devel perl-App-cpanminus \
    perl-Test-Most blas-devel atlas-devel lapack-devel libpng12 libpng12-devel \
    perl-XML-Simple perl-JSON csh gcc gcc-c++ make binutils gd gsl-devel git graphviz \
    java-1.7.0-openjdk perl-Archive-Zip perl-CGI curl perl-CGI-Session \
    perl-CPAN-Meta-YAML perl-DBI perl-Data-Dumper perl-GD perl-IO-Compress \
    perl-Module-Build perl-XML-LibXML perl-XML-Parser perl-XML-SAX perl-XML-SAX-Writer \
    perl-XML-Twig perl-XML-Writer perl-YAML perl-PerlIO-gzip libstdc++-static \
    cairo-devel openssl-devel openssl-static libssh2-devel libcurl-devel \
    wget rsync bzip2 bzip2-devel xz-devel time zip unzip which perl-CPAN \
    perl-LWP-Protocol-https cronie gnuplot gdb perl-JSON-XS perl-IO-Socket-IP \
    texlive texinfo libgfortran.x86_64 java-1.7.0-openjdk-devel boost-devel \
    libxml2-devel libXScrnSaver gtk3 perl-XML-DOM

  2. Update perl tools:

    sudo cpanm App::cpanoutdated
cpan-outdated -p | sudo cpanm

  3. Install perl modules by cpanm:

    sudo cpanm -f Bio::Perl Bio::SearchIO::hmmer3 Net::Ping File::Which
sudo cpanm Graph Time::Piece Hash::Merge PerlIO::gzip Heap::Simple::XS File::Next
sudo cpanm Algorithm::Munkres Archive::Tar Array::Compare Clone Convert::Binary::C
sudo cpanm HTML::Template HTML::TableExtract List::MoreUtils PostScript::TextBlock
sudo cpanm SOAP::Lite SVG SVG::Graph Set::Scalar Sort::Naturally Spreadsheet::ParseExcel
sudo cpanm CGI::Simple GraphViz XML::Parser::PerlSAX XML::Simple Term::ReadKey
sudo cpanm Spreadsheet::WriteExcel

  4. Install package for httpd for EDGE UI:

    sudo yum -y install httpd
sudo systemctl enable httpd && sudo systemctl start httpd

  5. Install packages for user management system:

    sudo yum -y install sendmail mariadb-server mariadb php phpMyAdmin tomcat
sudo systemctl enable tomcat && sudo systemctl start tomcat

  6. Configure firewall for ssh, http, https, and smtp:

    sudo firewall-cmd --permanent --add-service=ssh
sudo firewall-cmd --permanent --add-service=http
sudo firewall-cmd --permanent --add-service=https
sudo firewall-cmd --permanent --add-service=smtp
sudo firewall-cmd --reload

  7. Disable SELinux:

    As root edit /etc/selinux/config and set SELINUX=disabled

    Restart the server to make the change