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gbrowse是一个基因组数据可视化工具。利用它，您见建构自己的基因组浏览器。目前，利用这个工具，实现的基因组可视化有Rice genome browser 、Rat genome browser 和Pneumoniae 等。

一、系统和环境：
操作系统linux，建议采用debian类系统，理想的如ubuntu系统。以下的安装方式都是基于BioInfoserv4.0/ubuntu 10.04环境。

二、应用环境和库文件：

1、网页服务器：apache2/lighttpd

sudo apt-get install apache2 libapache2-mod-perl2 libapache2-mod-perl2-dev

2、perl和bioperl解释器：

sudo apt-get install libarchive-zip-perl libarchive-tar-perl bioperl bioperl-run libmodule-build-perl libio-string-perl libcapture-tiny-perl libcgi-session-perl libwww-perl libstatistics-descriptive-perl libjson-perl libjson-any-perl libapache2-mod-fastcgi libfcgi-perl libsvg-perl libtemplate-perl

3、libgd2库文件：

sudo apt-get install libgd2-xpm-dev libgd-gd2-perl libbio-graphics-perl

4、安装mysql数据库及其管理工具：

sudo apt-get install mysql-server phpmyadmin mysql-client libdbd-mysql-perl libmysqlclient-dev

5、其他软件（用于获取包和解包，建立文档连接关系）：

sudo apt-get install wget cvs subversion libc6-dev build-essential libpng12-dev ncftp inkscape

三、安装GBrowse

GBrowse的下载地址在http://sourceforge.net/projects/gmod/ ... neric%20Genome%20Browser/，选择需要下载的版本。低版本对其他包的依赖性小一些，而高版本需要多一些。以2.03为例，执行下面命令安装：

perl Makefile.PL

在执行perl Makefile.PL时，终端会显示不满足的依赖包情况。

1、依赖性包/文件：

A、对于2.03的安装，先执行下面命令安装依赖性包：

sudo apt-get install libfile-nfslock-perl libdb-file-lock-perl libnet-openid-consumer-perl libnet-smtp-ssl-perl libfile-temp-perl

B、对于2.03，Safe::World是必须的，尽管ubuntu系统下libbio-graphics-perl提供了相应的功能模块，但是似乎不能满足其要求，会出现一下错误：

#############################################################
perl Makefile.PL
# running Build.PL
Checking prerequisites...
  recommends:
    *  Safe::World is not installed

ERRORS/WARNINGS FOUND IN PREREQUISITES.  You may wish to install the versions
of the modules indicated above before proceeding with this installation

Run 'Build installdeps' to install missing prerequisites.

Creating new 'MYMETA.yml' with configuration results
Creating new 'Build' script for 'GBrowse' version '2.03'
Now run:
  ./Build test
  ./Build demo          (optional)
  ./Build install       (as superuser/administrator)
        -or-
  ./Build install_slave (optional, for slave installations)

Other useful targets:
  ./Build register      (to register your copy of GBrowse)
  ./Build reconfig      (to reconfigure install locations)
  ./Build demostop      (to stop the demo)
#############################################################

C、为此，单独下载Safe-World-0.14.tar.gz（文件在此下载）。解压该压缩文档，然后在解压目录中执行命令安装Safe-World：

   perl Makefile.PL
   make
   make test
   sudo make install

随即，执行以下命令，创建连接（否则2.03安装时依然会报错）：
sudo ln -s /usr/local/shareperl/5.10.1/Bio /usr/share/perl/5.10.1/Bio
sudo ln -s /usr/local/share/perl/5.10.1/Safe /usr/share/perl/5.10.1/Safe
sudo ln -s /usr/local/share/perl/5.10.1/GD /usr/share/perl/5.10.1/GD
################################################

完成了以上的依赖包安装后，就可以真正开始2.03的安装了：

perl Makefile.P
make
make test
sudo make install

此时，您会看到以下显示：

/usr/bin/perl Build --makefile_env_macros 1 install
NOTE: Run ./Build reconfig to change existing configuration.
Building GBrowse
Files found in blib/arch: installing files in blib/lib into architecture dependent library tree
Installing /var/www/cgi-bin/gb2/gbrowse_details
Installing /var/www/cgi-bin/gb2/gbrowse_login
Installing /var/www/cgi-bin/gb2/gbrowse_syn
Installing /var/www/cgi-bin/gb2/gbrowse_gmap
Installing /var/www/cgi-bin/gb2/gbrowse
Installing /var/www/cgi-bin/gb2/gbrowse_img
Installing /var/www/cgi-bin/gb2/gbgff
Installing /var/www/gbrowse2/databases/pop_demo/pop_demo.gff3
Installing /var/www/gbrowse2/databases/yeast_scaffolds/chr1.fa
Installing /var/www/gbrowse2/databases/yeast_scaffolds/chromosomes.gff3
Installing /var/www/gbrowse2/databases/yeast_scaffolds/chr2.fa
...............................................
Installing /var/www/gbrowse2/general_help.html
Installing /var/www/gbrowse2/index.html
Installing /var/www/gbrowse2/annotation_help.html
Installing /var/www/gbrowse2/gmod_cog.jpeg
Installing /var/www/gbrowse2/gbrowse_karyotype_help.html
Installing /var/www/gbrowse2/general_help.html.zh
Installing /var/www/gbrowse2/gbrowse_syn_help.html
Installing /var/www/gbrowse2/tutorial/tutorial.css
Installing /var/www/gbrowse2/tutorial/tutorial.phyTreeEdit.html
Installing /var/www/gbrowse2/tutorial/tutorial.html
Installing /var/www/gbrowse2/tutorial/bin/reformat.pl
Installing /var/www/gbrowse2/tutorial/bin/expression_levels.pl
..............................................
Installing /var/www/gbrowse2/images/spinner.gif
Installing /var/www/gbrowse2/images/backgrounds/steel.jpg
Installing /var/www/gbrowse2/images/backgrounds/lrock005.jpg
Installing /var/www/gbrowse2/images/backgrounds/cloud.jpg
...................................
Installing /var/www/gbrowse2/css/karyotype.css
Installing /var/www/gbrowse2/css/tracks.css
Installing /var/www/gbrowse2/css/titlebar-safari.css
........................................
Installing /var/www/gbrowse2/js/slider.js
Installing /var/www/gbrowse2/js/login.js
Installing /var/www/gbrowse2/js/yahoo-dom-event.js
...........................
Installing /etc/gbrowse2/languages
Installing /etc/gbrowse2/themes
...........................
***INSTALLATION COMPLETE***
Load http://localhost/gbrowse2 for demo and documentation

很显然安装完成，您可打开http://localhost/gbrowse2浏览安装结果了。至于低版本的gbrowse，安装结果可能在/var/www/gbrowse下，浏览地址为http://localhost/gbrowse。
而且，您可打开http://localhost/gbrowse2/tutorial/tutorial.html查看管理员的进一步配置工作。

2、安装新的数据：

首先，需要在/var/www/gbrowse2/databases中建立相应的数据库名称。例如建立肺炎链球菌的数据，则在/var/www/gbrowse2/databases建立S.pneumoniae

随后，采用命令： chmod go+rwx S.pneumoniae修改其属性。具体的数据格式在/var/www/gbrowse2/tutorial/data_files有示范：

volvox_all.gff3          
volvox_array.gff3        
volvox_bacs.gff3         
volvox_domains.gff3      
volvox_est_targets.gff3  
volvox_est.gff3          
volvox_geneproducts.gff3 
volvox_genes_simple.gff3
volvox_genes.gff3        
volvox_matches.gff3
volvox_microarray.gff3
volvox_microarray.wig
volvox_phyloalign_wigentries.gff3
volvox_phyloalign.gff3
volvox_remarks.gff3
volvox_trace.gff3
volvox.gff3
volvox.fa                
volvox_all.fa            
volvox_phyloalign.fa

您可将手里已有的数据按照示范中的格式进行加工后，拷贝到/var/www/gbrowse2/databases对应的目录中。

然后，编写相应GBrowse的配置文件S.pneumoniae.conf(编写完毕，拷贝到/etc/gbrowse2），大致的格式如下：

############################################################
[GENERAL]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
        -dir '/var/www/gbrowse2/databases/S.pneumoniae'

# just the basic track dumper plugin
plugins     = TrackDumper

# list of tracks to turn on by default
default features = ExampleFeatures

# size of the region
region segment         = 10000

# examples to show in the introduction
examples = ctgA

# feature to show on startup
initial landmark = ctgA:5000..10000

########################
# Default glyph settings
########################

[TRACK DEFAULTS]
glyph         = generic
height        = 10
bgcolor       = lightgrey
fgcolor       = black
font2color    = blue
label density = 25
bump density  = 100
# where to link to when user clicks in detailed view
link          = AUTO

################## TRACK CONFIGURATION ####################
# the remainder of the sections configure individual tracks
###########################################################

[ExampleFeatures]
feature      = remark
glyph        = generic
stranded     = 1
bgcolor      = blue
height       = 10
key          = Example Features
##########################################################

最后，在/etc/gbrowse2/GBrowse.conf主配置文件中，加入这样的字样（注意保留一行空行）：

[S.pneumoniae]
description  = S.pneumoniae database
path         = S.pneumoniae.conf

3、浏览注释数据：

http://localhost/cgi-bin/gb2/gbrowse/S.pneumoniae