2. System requirements

NOTE: There is a demo version of EDGE, found on https://bioedge.lanl.gov/edge_ui/ is run on our own internal servers and is recommended only for testing and demo purposes only.

The current version of the EDGE pipeline has been extensively tested on a Linux Server with Ubuntu 14.04 and CentOS 7 operating system and will work on 64bit Linux environments. Perl v5.8 or above is required.

2.1. Hardware Requirements

Due to the involvement of several high memory and high cpu consuming steps

Minimum requirement: 16GB memory and at least 8 computing CPUs.

A higher computer spec is strongly recommended: 256GB memory and 64 computing CPUs.

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 14.04 or Centos 7, it may have differnt packages/libraries name and the newer complier (gcc5) on newer OS (ex: Ubuntu 16.04) may fail on compling some of thirdparty bioinformatics tools. We would suggest to use EDGE VMware image or Docker container.

2.2. Ubuntu 14.04

1. Install build essential libraries and dependancies:

   sudo apt-get -y update
   
   sudo apt-get install -y build-essential libreadline-gplv2-dev libx11-dev \
           libxt-dev libgsl0-dev libfreetype6-dev libncurses5-dev gfortran \
           inkscape libwww-perl libxml-libxml-perl libperlio-gzip-perl  \
           zlib1g-dev zip unzip libjson-perl libpng12-dev cpanminus default-jre \
           firefox wget curl csh liblapack-dev libblas-dev libatlas-dev \
           libcairo2-dev libssh2-1-dev libssl-dev libcurl4-openssl-dev bzip2 \
           bioperl rsync libbz2-dev liblzma-dev time
   

A Note about python:note:

Anaconda2 a scientific python package will be installed by INSTALL.sh.

2. Install Apache2 for EDGE UI:

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

3. Install packages for user management system:

   sudo apt-get install sendmail mysql-client mysql-server phpmyadmin tomcat7
   

2.3. CentOS 7

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
   

A Note about python:note:

Anaconda2 a scientific python package will be installed by INSTALL.sh.

2. Update existing perl tools:

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   cpan-outdated -p | cpanm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

3. Install perl modules by cpanm:

   sudo cpanm -f Bio::Perl
   sudo cpanm Graph Time::Piece
   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
   

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