Difference between revisions of "GBrowse 2.0 Prerequisites"
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==Installing Bio::Graphics and BioPerl==
==Installing Bio::Graphics and BioPerl==
You should the Git versions of Bio::Graphics and Bio::Perl:
Revision as of 02:30, 31 July 2014
Before installing GBrowse 2.0, you will need to install some prerequisites on your system. Most prerequisites come as prepackaged binaries which can be installed from the command line or via GUI tools. This document describes the prerequisites for Linux, Mac OSX, and Microsoft Windows systems.
The following prerequisites are needed to run GBrowse on Linux systems:
Applications and Libraries
Although not required for basic operation, you will probably want at least one relational database backend. One or both of:
Those who want to obtain the best performance should consider the mod_perl, or FastCGI Apache modules:
Those who wish to generate publication-ready PDFs from GBrowse tracks should install the inkscape package:
These applications can be installed from source code or from binary packages using one of the binary packaging systems described below.
If you use a modern Linux distribution, most prerequisites are available as binary packages. There are two common package managers, Debian (DEB) and RedHat Package Manager (RPM). The next section shows you how to use command-line package management tools to install the prerequisites.
DEB Systems (apt)
Distributions on which apt is installed by default include Ubuntu (and its variants), Debian, and Mint. To install all prerequisites except for BioPerl, run the following commands as the root or using sudo (comments begin with the # sign). Some of these packages may already be installed on your system.
#Utilities to help with fetching components distributed in source code sudo apt-get install wget subversion git-core libc6-dev build-essential libgd2-noxpm-dev #apache2 with acceleration sudo apt-get install apache2 libapache2-mod-fcgid libapache2-mod-perl2 #fast lightweight database for managing user accounts sudo apt-get install sqlite3 libdbd-sqlite3-perl #Perl libraries sudo apt-get install libmodule-build-perl libio-string-perl \ libcapture-tiny-perl libcgi-session-perl libwww-perl libstatistics-descriptive-perl \ libjson-perl libjson-any-perl libsvg-perl perl-doc libtemplate-perl libgd-gd2-perl libgd-svg-perl \ libdata-stag-perl libterm-readkey-perl libhttp-daemon-perl # optional libraries for using MySQL and PostgreSQL backends sudo apt-get install mysql-server mysql-client libdbd-mysql-perl libmysqlclient-dev postgresql libdbd-pg-perl # optional libraries for e-mail-based user registration and OpenID logins sudo apt-get install libdigest-sha-perl libssl-dev libmath-bigint-gmp-perl \ libnet-openid-consumer-perl libnet-smtp-ssl-perl libauthen-sasl-perl libcrypt-ssleay-perl
All these installation steps must be executed as root (shown here using sudo).
Packaged versions of BioPerl contain a bug that prevents GBrowse from displaying DNA sequences from in-memory databases. Install Bioperl from source code this way:
git clone https://github.com/bioperl/bioperl-live.git cd bioperl-live perl Build.PL ./Build test sudo ./Build install
Ubuntu 10.04/11.04 Issue
The binary version of the GD Perl module that is packaged for Ubuntu 10.04 (Lucid Lynx) and 11.04 (Natty Narwhal) contains a bug that causes BioPerl to fail several of its tests, blocking GBrowse installation. To fix:
sudo apt-get remove libgd-gd2-perl sudo apt-get install libgd2-noxpm-dev sudo perl -MCPAN -e 'install GD'
Then proceed to install Bio::Graphics::Browser2 from the CPAN shell as described in GBrowse 2.0 Install HOWTO.
RPM Systems (yum)
This includes Fedora, RedHat, SuSE, Mandriva, PCLinuxOS, and CentOS. Most of these distributions have the command line package management tool yum which is used in the following command examples. These commands will need to be run as root (or equivalently by using sudo in the manner shown above):
# build utilities yum install make gcc gmp-devel #Utilities to help with fetching components distributed in source code yum install wget git #apache2 yum install httpd mod_fcgid fcgi-perl # various Perl modules yum install perl-GD perl-Module-Build perl-CPAN perl-IO-String perl-Capture-Tiny perl-CGI-Session \ perl-JSON perl-JSON-Any perl-libwww-perl perl-DBD-SQLite perl-File-NFSLock perl-Net-SMTP-SSL \ perl-Crypt-SSLeay perl-Net-SSLeay perl-Template-Toolkit # bioperl yum install perl-bioperl perl-Bio-Graphics #optionally... yum install mysql-server mysql-libs perl-DBD-MySQL yum install postgresql postgresql-server perl-DBD-Pg yum install inkscape yum install perl-GD-SVG
Installing Bio::Graphics and BioPerl
You should use the Git versions of Bio::Graphics and Bio::Perl. As of 30 July 2014, the CPAN versions contained bugs that interfere with the GBrowse dispaly:
git clone https://github.com/bioperl/bioperl-live.git cd bioperl-live perl Build.PL ./Build test sudo ./Build install git clone https://github.com/GMOD/Bio-Graphics.git cd Bio-Graphics perl Build.PL ./Build test sudo ./Build install
You're done installing prerequisites! You can now go back to the GBrowse 2.0 Install HOWTO, and follow the installation instructions for your platform.
These instructions apply to Macintosh OSX version 10.5, using the fink binary installer. First, download and install Fink. Next open up the terminal window and type the following commands as the root user or with sudo (as shown):
#Utility to help components distributed in source code sudo fink install wget #libgd2 and its Perl library sudo fink install gd2 gd2-bin sudo perl -MCPAN -e 'install GD' #other Perl modules sudo perl -MCPAN -e 'install IO::String' sudo perl -MCPAN -e 'install CGI::Session' sudo perl -MCPAN -e 'install JSON' sudo perl -MCPAN -e 'install JSON::Any' #optionally. sudo fink install mysql '''more to come here''' sudo perl -MCPAN -e 'install GD::SVG'
this section is unfinished
If it isn't already activated, turn the Apache server on by activating Control Panel->Sharing->Web Sharing.
Mac Ports Way
First, download and install MySQL Community Server form http://dev.mysql.com/downloads/mysql/.
You can download and install macports from http://www.macports.org/.
Edit your .profile '/Users/youname/.profile'
export DYLD_LIBRARY_PATH=/usr/local/mysql-5.5.9-osx10.6-x86_64/lib:$DYLD_LIBRARY_PATH export PATH=/usr/local/mysql/bin:/opt/local/bin:/opt/local/sbin:/usr/local/bin/:$PATH
Then, logout and login.
# sudo port install perl5 # sudo port install apache2 # sudo port install p5-gd # sudo port install git-core
Using cpan install these modules
GD::SVG SVG CGI DBI DBD::mysql DBD::SQLite Statistics::Descriptive Data::Stag GD::Graph GD::Graph::smoothlines Statistics::Lite Statistics::LineFit Compress::Zlib IO::Zlib Config::Simple Pod::Usage Algorithm::Cluster
#git clone git://github.com/bioperl/bioperl-live.git # cd bioperl-live # perl Build.PL # ./Build test # sudo ./Build install
GBrowse depends on the following standard Perl libraries:
- Bio::Perl (version 1.6.0 or higher)
In addition, the following optional Perl libraries are recommended:
- GD::SVG (for PDFs and editable high-resolution images)
- DBI (for relational database access)
- DBD::mysql (for MySQL database backends)
- DBD::Pg (for PostgreSQL database access)
- DB_File::Lock (for load balancing in rendering slavesstrongly)
- File::NFSLock (if two or more servers are sharing the same NFS-mounted directory for sessions)
- Template (to run the population allele frequency visualization demo)
- Crypt::SSLeay, Math::BigInt, Net::OpenID::Consumer, Net::SMTP::SSL (for user account registration)
- Note: The Math::BigInt and Net::OpenId::Consumer library installation tests will run very slowly unless supported by the Math::BigInt::GMP or Math::BigInt::Pari libraries. It is suggested that you install these libraries before trying to install Math::BigInt and Net::OpenId::Consumer.