Difference between revisions of "GBrowse Tutorial"

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{| class="tutorialheader"
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There are several [[GBrowse]] tutorials:
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| align="right" | {{#icon: 2010SummerSchoolAmericas300.png|2010 GMOD Summer School - Americas||2010 GMOD Summer School - Americas}}
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| {{TutorialTitleLine|[[GBrowse]]}}<br />
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[[2010 GMOD Summer School - Americas]]<br />
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May 6-9, 2010<br />
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[[User:Scott|Scott Cain]]
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__NOTITLE__
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; [[GBrowse Tutorial 2012|GBrowse tutorial from 2012 GMOD Summer School]]
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: This tutorial was taught by [[User:Scott|Scott Cain]] at 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.
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; [[GBrowse Tutorial 2010|GBrowse tutorial from 2010 GMOD Summer School]]
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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}}.
  
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<div class="emphasisbox">
 
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<center><span style="font-size: 140%">There are several [[GBrowse]] [[:Category:Tutorials|tutorials]]:</span></center>
 
 
; [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.
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; [[GBrowse NGS Tutorial]]
 
; [[GBrowse NGS Tutorial]]
 
: 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.
 
: 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.
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; This tutorial
 
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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}}.
 
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</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.
 
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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/2010/SummerSchoolAmericas/GMODCourse2010Day1.vmwarevm.tar.gz Starting&nbsp;Image]<br>
 
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[ftp://ftp.gmod.org/pub/gmod/Courses/2010/SummerSchoolAmericas/GMODCourse2010Day2.vmwarevm.tar.gz  Ending Image]<br />
 
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|-
 
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! Logins
 
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|-
 
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|
 
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{| class="wikitable"
 
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! Purpose
 
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! Username
 
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! Password
 
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|-
 
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| Shell
 
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| gmod
 
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| gmodamericas2010
 
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|-
 
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| MySQL
 
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| root
 
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| gmodamericas2010
 
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|}
 
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|}
 
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|}
 
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= Caveats =
 
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{{TutorialCaveats}}
 
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=Prerequisites=
 
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Installed before using apt or cpan.
 
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=Install GBrowse=
 
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Easily installed via the cpan shell:
 
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  <span class="enter">sudo cpan</span>
 
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  cpan> <span class="enter">install Bio::Graphics::Browser2</span>
 
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Which gets all of the prereqs that aren't installed on the machine.
 
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=Tutorial=
 
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Go to http://localhost/gbrowse
 
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=Basic [[Chado]] Configuration (if we have time)=
 
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{{CPAN|Bio::DB::Das::Chado}} was installed when we created the image, but I've since released a new version, so we can install the new version with the cpan shell:
 
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  <span class="enter">sudo cpan</span>
 
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  cpan> <span class="enter">install Bio::DB::Das::Chado</enter>
 
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Simple config file in <tt>/etc/gbrowse2/pythium.conf</tt>
 
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Some simple tweaks and additions:
 
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*fix the dbi string
 
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*add nucleotide matches
 
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*strip out stuff that is in <tt>/etc/gbrowse2/GBrowse.conf</tt>
 
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==Materialized views for searching==
 
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Chado comes with a tool to materialize views written by developers at the [[:Category:SGN|SOL Genomics Network (SGN)]].  A materialized view is faster (at the expense of more disk space) to search than a regular view (which is really a query over potentially several tables).  To create a materialized view that makes searching a GBrowse [[Chado]] instance a faster, we can do this:
 
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  <span class="enter">gmod_materialized_view_tool.pl -c</span>
 
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which will ask us several obscure questions for which we need to provide obscure answers:
 
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  Give your materialized view a name (word characters only):
 
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  <span class="enter">all_feature_names</span>
 
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  Where will this MV be located? (schemaname.tablename):
 
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  <span class="enter">public.all_feature_names</span>
 
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  A view with this name already exists; do you want to replace it
 
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  with a materialized view? [y|n]
 
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  <span class="enter">y</span>
 
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  How often, in seconds, should the MV be refreshed?
 
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  You can also type 'daily', 'weekly', 'monthly' (30 days), or 'yearly' (365 days):
 
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  <span class="enter">weekly</span>
 
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  Enter specifications for the materialized view, OR provide a file in which
 
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  the specs are written ('? for help):
 
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  <span class="enter">feature_id integer,name varchar(255)</span>
 
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  Enter the SQL query for the materialized view,
 
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  or a file containing only the query:
 
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  <span class="enter">SELECT feature_id,CAST(substring(uniquename from 0 for 255) as varchar(255)) as name FROM feature UNION SELECT feature_id, name FROM feature where name is not null UNION SELECT fs.feature_id,s.name FROM feature_synonym fs, synonym s WHERE fs.synonym_id = s.synonym_id</span>
 
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  Enter a comma separated list of fields to index (or return for none):
 
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  <span class="enter">feature_id,name</span>
 
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  Enter the SQL queries for special indexes,
 
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  or a file containing only the query (or return for none):
 
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  <span class="enter">create index all_feature_names_lower_name on all_feature_names (lower(name))</span>
 
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  Enter 'y' to confirm, 'n' to re-enter data:
 
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  <span class="enter">y</span>
 
  
 
[[Category:Tutorials]]
 
[[Category:Tutorials]]
 
[[Category:GBrowse]]
 
[[Category:GBrowse]]

Revision as of 22:37, 4 September 2012

There are several GBrowse tutorials:

GBrowse tutorial from 2012 GMOD Summer School
This tutorial was taught by Scott Cain at 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.
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