Difference between revisions of "GMOD - Getting Started"

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GMOD is a large project with many components and this page aims to give you some pointers on where you can start.
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== Useful Pages ==
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* [[GMOD_for_the_Biologist|GMOD for the Biologist]] is a broad introduction, aimed at biologists.  This is an excellent place to start.
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* [[GMOD Components]] is a complete list of the components in GMOD.  This list can appear daunting, but it gives you a good idea of what sorts of things are available from GMOD.
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** If you already know the specific component you want to use (''e.g.'' [[GBrowse]], [[Apollo]], [[CMap]], ...) you can type the component name in the search box and go directly to the page for that component.
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* [[ParameciumDB]] describes how ParameciumDB implemented GMOD at their web site.
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* [[Chado_-_Getting_Started|Getting Started with Chado]] discusses GMOD's relational database schema.  Chado is useful for organizing your data and is also integrated with several other GMOD components.
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* [[Computing Requirements]] discusses what sort of computing support you will need to install and run GMOD components.
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==Getting Advice==
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If you need advice or help you can write to one of a number of [[GMOD_Mailing_Lists|GMOD mailing lists]], these tend to focus on more technical aspects. Another good resource is the [[GMOD_Help_Desk|GMOD Help Desk]] - feel free to write them with questions on any type, they are tasked with providing support to newcomers and experts alike.
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See [[Finding support]] for more information.
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 +
 
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==Installation==
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{{NeedsEditing}}
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'''Actually, this material needs to be moved to its own page.'''
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There are different ways to install the subset of GMOD components needed to get a working organism database.
 +
 
 +
===Using VMWare Images===
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VMWare images provide a simple way to try GMOD software without installing it on your local machine.  You download [http://www.vmware.com/products/player/ VMWare Player] and an virtual machine image that contains GMOD software pre-installed and configured.  This image then runs as a stand-alone computer inside the virtual machine provided by VMWare Player.  This option is currently in development, see the [[VMWare HOWTO]] for more information.
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===Using ''yum'' on Unix===
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One easy way assumes that you have a computer with [http://isoredirect.centos.org/centos/4/isos/ CentOS 4] freshly installed so that you can take advantage of several 'short cut' packages that have been prebuilt for that operating system and are available from [http://www.biopackages.net/ biopackages.net]. See the [[Biopackages HOWTO]] for more information on this option.
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===Installing from Source===
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The harder way is for any other OS and requires just about everything to be built from source. A list of stable releases is found here: http://sourceforge.net/project/showfiles.php?group_id=27707.
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===Getting the Latest & Greatest Version by CVS===
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There are many new features in the development versions which have not been released yet. To get the latest version of a [[GMOD_Components|GMOD component]] you can use anonymous CVS. Here is the recipe:
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>cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
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CVS password: <hit return>
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>cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co <component>
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For a list of all the GMOD components that can be accessed by CVS, or ''checked out'', see http://sourceforge.net/project/showfiles.php?group_id=27707.
  
 
[[Category:Needs Editing]]
 
[[Category:Needs Editing]]
 
[[Category:Help]]
 
[[Category:Help]]

Revision as of 17:34, 26 May 2008

GMOD is a large project with many components and this page aims to give you some pointers on where you can start.


Useful Pages

  • GMOD for the Biologist is a broad introduction, aimed at biologists. This is an excellent place to start.
  • GMOD Components is a complete list of the components in GMOD. This list can appear daunting, but it gives you a good idea of what sorts of things are available from GMOD.
    • If you already know the specific component you want to use (e.g. GBrowse, Apollo, CMap, ...) you can type the component name in the search box and go directly to the page for that component.
  • ParameciumDB describes how ParameciumDB implemented GMOD at their web site.
  • Getting Started with Chado discusses GMOD's relational database schema. Chado is useful for organizing your data and is also integrated with several other GMOD components.
  • Computing Requirements discusses what sort of computing support you will need to install and run GMOD components.

Getting Advice

If you need advice or help you can write to one of a number of GMOD mailing lists, these tend to focus on more technical aspects. Another good resource is the GMOD Help Desk - feel free to write them with questions on any type, they are tasked with providing support to newcomers and experts alike.

See Finding support for more information.


Installation

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

Actually, this material needs to be moved to its own page.

There are different ways to install the subset of GMOD components needed to get a working organism database.

Using VMWare Images

VMWare images provide a simple way to try GMOD software without installing it on your local machine. You download VMWare Player and an virtual machine image that contains GMOD software pre-installed and configured. This image then runs as a stand-alone computer inside the virtual machine provided by VMWare Player. This option is currently in development, see the VMWare HOWTO for more information.

Using yum on Unix

One easy way assumes that you have a computer with CentOS 4 freshly installed so that you can take advantage of several 'short cut' packages that have been prebuilt for that operating system and are available from biopackages.net. See the Biopackages HOWTO for more information on this option.

Installing from Source

The harder way is for any other OS and requires just about everything to be built from source. A list of stable releases is found here: http://sourceforge.net/project/showfiles.php?group_id=27707.


Getting the Latest & Greatest Version by CVS

There are many new features in the development versions which have not been released yet. To get the latest version of a GMOD component you can use anonymous CVS. Here is the recipe:

>cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod login
CVS password: <hit return>
>cvs -d :pserver:anonymous@gmod.cvs.sourceforge.net:/cvsroot/gmod co <component>

For a list of all the GMOD components that can be accessed by CVS, or checked out, see http://sourceforge.net/project/showfiles.php?group_id=27707.