Difference between revisions of "GBrowse Tutorial"

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There are several [[GBrowse]] tutorials:
  
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; [[GBrowse Tutorial 2012|GBrowse tutorial from 2013 GMOD Summer School]]
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: This tutorial was taught by [[User:Scott|Scott Cain]] at the [[2013 GMOD Summer School]] and the [[2012 GMOD Summer School]]. It demonstrates setting up, configuring and using [[GBrowse]] with some sample data. GBrowse is provided on an Amazon Machine Image: see [[Cloud|GMOD in the Cloud]] for more information on getting a GMOD AMI.
  
{| class="tutorialheader"
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; [[GBrowse Tutorial 2010|GBrowse tutorial from 2010 GMOD Summer School]]
| align="right" | {{#icon: GMOD2009Europe170.png|2009 GMOD Summer School - Europe||2009 GMOD Summer School - Europe}}
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: This tutorial was originally taught by [[User:Scott|Scott Cain]] at the [[2010 GMOD Summer School - Americas]].  It walks you through setting up and running [[GBrowse]] with some sample data.  It provides a [[VMware]] image to work on, and relies heavily on the {{GBrowseAdminTutorialLink|GBrowse Administration Tutorial}}.
| {{TutorialTitleLine|[[GBrowse]]}}<br />
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[[2009 GMOD Summer School - Europe]]<br />
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4 August 2009<br />
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[[User:Scott|Scott Cain]]
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|}
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<div class="emphasisbox">
 
<span style="font-size: 120%">There are several [[GBrowse]] [[:Category:Tutorials|tutorials]]:</span>
 
 
; [http://www.openhelix.com/gbrowse GBrowse User Tutorial] at [http://www.openhelix.com OpenHelix]
 
; [http://www.openhelix.com/gbrowse GBrowse User Tutorial] at [http://www.openhelix.com OpenHelix]
 
: Demonstrates the GBrowse ''user'' interface.
 
: Demonstrates the GBrowse ''user'' interface.
  
; [http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/docs/tutorial/tutorial.html?pathrev=stable GBrowse Administration Tutorial]
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; {{GBrowseAdminTutorialLink|GBrowse Administration Tutorial}}
: Step by step guide on how to configure and load data into GBrowse.
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: Step by step guide on how to configure and load data into [[GBrowse]].  Administration tutorials are available for both the {{GBrowseAdminTutorialLink|current version}}, and the earlier {{GBrowse1AdminTutorialLink|1.x versions}}.
  
; This tutorial
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; [[GBrowse NGS Tutorial]]
: This tutorial was originally taught by [[User:Scott|Scott Cain]] at the [[2009 GMOD Summer School - Europe]]. It walks you through setting up and running the [[MAKER]] genome annotation pipeline with some sample dataIt provides a [[VMware]] image to work on, and relies heavily on the [http://gmod.cvs.sourceforge.net/*checkout*/gmod/Generic-Genome-Browser/docs/tutorial/tutorial.html?pathrev=stable GBrowse Administration Tutorial].
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: Instructions on how to visualize [[next generation sequencing]] data in GBrowse using [http://samtools.sourceforge.net SAMtools].  The tutorial includes a starting [[VMware]] image, and uses the example data that comes with SAMtools.
  
; Note:
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; [http://youtu.be/jxA6VMN97Y8 GBrowse video tutorial]
This tutorial was also taught at the [[2009 GMOD Summer School - Americas]], but the notes and the VMware system image are for the [[2009 GMOD Summer School - Europe|Europe course]].
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: Produced by [http://eupathdb.org EuPathDB]; please direct praise and thanks to them!
</div>
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__TOC__
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= VMware =
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{|
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| valign="top" |This tutorial was taught using a [[VMware]] system image as a starting point.  If you want to start with that same system, download and install the ''Starting'' image.  There is also an ''Ending'' image for this tutorial, which contains the system after this tutorial (and the [[GBrowse_syn Tutorial]]) have been finished.
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'''''See [[VMware]] for what software you need to use a VMware system image, and for directions on how to get the image setup and running on your machine.'''''
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|
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{| style="margin-left: 1em; margin-top: 0; " class="wikitable"
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! Download
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|-
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| align="center" | [ftp://ftp.gmod.org/pub/gmod/Courses/2009/SummerSchoolEurope/GmodSumSch2009EU2.zip Starting&nbsp;Image]<br>
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[ftp://ftp.gmod.org/pub/gmod/Courses/2009/SummerSchoolEurope/GmodSumSch2009EU3.tar.gz Ending Image]<br />
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----
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Username:&nbsp;gmod<br />Password: gmod
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|}
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|}
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= Caveats =
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{{TutorialCaveats}}
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[[Category:Tutorials]]
 
[[Category:Tutorials]]
 
[[Category:GBrowse]]
 
[[Category:GBrowse]]

Latest revision as of 17:10, 18 December 2013

There are several GBrowse tutorials:

GBrowse tutorial from 2013 GMOD Summer School
This tutorial was taught by Scott Cain at the 2013 GMOD Summer School and the 2012 GMOD Summer School. It demonstrates setting up, configuring and using GBrowse with some sample data. GBrowse is provided on an Amazon Machine Image: see GMOD in the Cloud for more information on getting a GMOD AMI.
GBrowse tutorial from 2010 GMOD Summer School
This tutorial was originally taught by Scott Cain at the 2010 GMOD Summer School - Americas. It walks you through setting up and running GBrowse with some sample data. It provides a VMware image to work on, and relies heavily on the GBrowse2 Admin Tutorial.
GBrowse User Tutorial at OpenHelix
Demonstrates the GBrowse user interface.
GBrowse2 Admin Tutorial
Step by step guide on how to configure and load data into GBrowse. Administration tutorials are available for both the GBrowse2 Admin Tutorial, and the earlier 1.x versions.
GBrowse NGS Tutorial
Instructions on how to visualize next generation sequencing data in GBrowse using SAMtools. The tutorial includes a starting VMware image, and uses the example data that comes with SAMtools.
GBrowse video tutorial
Produced by EuPathDB; please direct praise and thanks to them!