Difference between revisions of "GBrowse RPM HOWTO"

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RPM-based Linux distributions, including [http://fedoraproject.org/wiki/ Fedora Core] and [http://www.centos.org CentOS], can install GBrowse using the RPMs located at http://www.biopackages.net/. These can be installed using the [http://en.wikipedia.org/wiki/Yellow_dog_Updater_Modified yum] installer tool.
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{{NeedsEditing}}
  
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At the time of this writing (April 2007) complete RPMs through Fedora Core 2 are available, and supported architectures included 32- and 64-bit Power PC (Mac OS 10.4) and 32- and 64-bit intel platforms (Fedora Core and CentOS). Check back regularly for updates.
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'''Important note:''' The instructions below will install a relatively old version of GBrowse (1.54 I think).  To install a newer version, first install the Apache webserver (httpd) and libgd with yum:
  
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  sudo yum install gd-devel httpd
  
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=Preliminaries=
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and then follow the directions on [[GBrowse Install HOWTO|the main install page]] for using the net install script. If you don't want or need the 'bleating edge', just ignore this note.
  
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To configure yum to be aware of the Biopackages.net repository, add the following to your /etc/yum.conf file:
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=Biopackages=
  
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[biopackages-stable]
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RPM-based Linux distributions, including [http://fedoraproject.org/ Fedora] and [http://www.centos.org CentOS], can install GBrowse using the RPMs located at http://www.biopackages.net/. These can be installed using the [http://en.wikipedia.org/wiki/Yellow_dog_Updater_Modified yum] installer tool. For more information please see the [[Biopackages HOWTO]].
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name=BioPackages (Stable) for Fedora Core $releasever - $basearch
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baseurl=http://yum.biopackages.net/biopackages/stable/fedora/$releasever/$basearch/
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[biopackages-stable-noarch]
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=Preliminaries=
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name=BioPackages (Stable) for Fedora Core $releasever - noarch
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baseurl=http://yum.biopackages.net/biopackages/stable/fedora/$releasever/noarch/
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See the [[Biopackages HOWTO]] for the steps to setup Biopackages on your system.
  
 
=Installing Packages=
 
=Installing Packages=
  
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First, as root, freshen your local cache of yum header files. Yum will print something similar to what is below:  
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First, as root, freshen your local cache of yum header files. Yum will print something similar to what is below:
  
 
  % yum update
 
  % yum update
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  Server: BioPackages (Stable x86_64) for Fedora Core 2 - x86_64
 
  Server: BioPackages (Stable x86_64) for Fedora Core 2 - x86_64
 
  Server: BioPackages (Stable noarch) for Fedora Core 2 - x86_64
 
  Server: BioPackages (Stable noarch) for Fedora Core 2 - x86_64
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Server: BioPackages (Testing x86_64) for Fedora Core 2 - x86_64
 
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Server: BioPackages (Testing noarch) for Fedora Core 2 - x86_64
 
 
  Server: Fedora Core 2 - x86_64 - Released Updates
 
  Server: Fedora Core 2 - x86_64 - Released Updates
 
  Finding updated packages
 
  Finding updated packages
 
  Downloading needed headers
 
  Downloading needed headers
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  genome-Sce-annotation-gen 100% |=========================| 1.1 kB    00:00    
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  genome-Sce-annotation-gen 100% |=========================| 1.1 kB    00:00
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  genome-Sce-nib-0-S228C-3. 100% |=========================| 1.7 kB    00:00    
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  genome-Sce-nib-0-S228C-3. 100% |=========================| 1.7 kB    00:00
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  chado-Sce-0-S228C.0.003-2 100% |=========================| 2.0 kB    00:00    
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  chado-Sce-0-S228C.0.003-2 100% |=========================| 2.0 kB    00:00
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  genome-Sce-annotation-aff 100% |=========================| 1.2 kB    00:00    
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  genome-Sce-annotation-aff 100% |=========================| 1.2 kB    00:00
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  genome-Sce-0-S228C-3.2005 100% |=========================| 1.7 kB    00:00    
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  genome-Sce-0-S228C-3.2005 100% |=========================| 1.7 kB    00:00
  
 
Then install gbrowse:
 
Then install gbrowse:
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You can now visit the documentation and try out the example Yeast database by visiting http://localhost/gbrowse
 
You can now visit the documentation and try out the example Yeast database by visiting http://localhost/gbrowse
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NOTE: One problem with the RPM install is it currently installs gbrowse into it's own directory (e.g. /var/www/cgi-bin/gbrowse/).  This means that the yeast example referenced in http://localhost/gbrowse should actually point to http://localhost/cgi-bin/gbrowse/gbrowse/yeast_chr1.
  
 
=Authors=
 
=Authors=
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Some material cut and paste from www.biopackages.net, with permission from Allen Day.
 
Some material cut and paste from www.biopackages.net, with permission from Allen Day.
  
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[[Category:HOWTO]
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[[User:Boconnor|Brian O'Connor]] 12:12, 19 April 2007 (PDT)
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Updated the install description of Biopackages to use our new configuration RPMs.
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[[User:Boconnor|Brian O'Connor]] 12:18, 05 June 2007 (PDT)
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Added note about install path for gbrowse.
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[[Category:GBrowse]]
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[[Category:HOWTO]]
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[[Category:Linux]]

Latest revision as of 11:32, 28 October 2008

This page or section needs to be edited. Please help by editing this page to add your revisions or additions.

Important note: The instructions below will install a relatively old version of GBrowse (1.54 I think). To install a newer version, first install the Apache webserver (httpd) and libgd with yum: 

 sudo yum install gd-devel httpd

and then follow the directions on the main install page for using the net install script. If you don't want or need the 'bleating edge', just ignore this note.

Biopackages

RPM-based Linux distributions, including Fedora and CentOS, can install GBrowse using the RPMs located at http://www.biopackages.net/. These can be installed using the yum installer tool. For more information please see the Biopackages HOWTO.

Preliminaries

See the Biopackages HOWTO for the steps to setup Biopackages on your system.

Installing Packages

First, as root, freshen your local cache of yum header files. Yum will print something similar to what is below: 

% yum update
Gathering header information file(s) from server(s)
Server: Fedora Core 2 - x86_64 - Base
Server: BioPackages (Stable x86_64) for Fedora Core 2 - x86_64
Server: BioPackages (Stable noarch) for Fedora Core 2 - x86_64
Server: Fedora Core 2 - x86_64 - Released Updates
Finding updated packages
Downloading needed headers
genome-Sce-annotation-gen 100% |=========================| 1.1 kB    00:00
genome-Sce-nib-0-S228C-3. 100% |=========================| 1.7 kB    00:00
chado-Sce-0-S228C.0.003-2 100% |=========================| 2.0 kB    00:00
genome-Sce-annotation-aff 100% |=========================| 1.2 kB    00:00
genome-Sce-0-S228C-3.2005 100% |=========================| 1.7 kB    00:00

Then install gbrowse: 

% yum install gbrowse

You can now visit the documentation and try out the example Yeast database by visiting http://localhost/gbrowse

NOTE: One problem with the RPM install is it currently installs gbrowse into it's own directory (e.g. /var/www/cgi-bin/gbrowse/). This means that the yeast example referenced in http://localhost/gbrowse should actually point to http://localhost/cgi-bin/gbrowse/gbrowse/yeast_chr1.

Authors

Lincoln Stein 12:51, 17 April 2007 (EDT)

Some material cut and paste from www.biopackages.net, with permission from Allen Day.

Brian O'Connor 12:12, 19 April 2007 (PDT)

Updated the install description of Biopackages to use our new configuration RPMs.


Brian O'Connor 12:18, 05 June 2007 (PDT)

Added note about install path for gbrowse.

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