This page was last updated on Friday, 03-Nov-2017 15:26:51 CDT
Installation notes for GBrowse version xxx
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Prerequisites
http://gmod.org/wiki/GBrowse_2.0_Prerequisites
- 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 libfcgi-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
- I also found that I needed to install
$ sudo cpan Test::Most
- And it looked like I could install
$ sudo cpan Bio::SeqFeature::Lite Bio::DB::Sam Bio::ASN1::EntrezGene HTML::TableExtract Bio::Ext::Align
- For TopoView
sudo apt-get install libdb5.3-dev
sudo cpan BerkeleyDB
Installation
- 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:
$ cd /programinstallers/
- $ git clone https://github.com/bioperl/bioperl-live.git
- $ cd bioperl-live
- $ perl Build.PL
- $ ./Build test
- $ sudo ./Build install
- $
- $
- $