Difference between revisions of "GBrowse Tutorial"

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{{UnderConstruction}}
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There are several [[GBrowse]] tutorials:
{| class="tutorialheader"
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| align="right" | {{#icon: GMOD2009Europe170.png|2009 GMOD Summer School - Europe||2009 GMOD Summer School - Europe}}
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; [[GBrowse Tutorial 2012|GBrowse tutorial from 2013 GMOD Summer School]]
| {{TutorialTitleLine|[[GBrowse]]}}<br />
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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.
[[2009 GMOD Summer School - Europe]]<br />
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4 August 2009<br />
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; [[GBrowse Tutorial 2010|GBrowse tutorial from 2010 GMOD Summer School]]
[[User:Scott|Scott Cain]]
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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">
 
<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}}.
 
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; This tutorial
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: 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 data.  It 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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'''Note:''' This tutorial was also taught at the [[2009 GMOD Summer School - Americas]], but the notes and system image used here are from the [[2009 GMOD Summer School - Europe|Europe course]].
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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.  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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=Prerequisites=
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Most installed before using apt or cpan
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<div class="emphasisbox">
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Should be able to install Bio::Graphics via cpan like such:
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  cpan> install Bio::Graphics
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Weirdly, cpan thinks that BioPerl 1.6 is not installed yet, so it will install it, as well as updating Data::Stag (it will take a few minutes and requires cpan)
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(In hindsight, the apt-get of libgd-tools below ''might'' have fixed this problem.)
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</div>
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Instead get it the source from http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-Graphics-1.97.tar.gz
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If you download that from Firefox, it will put on the desktop.
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<bash>cd ~/Desktop
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tar xzvf Bio-Graphics-1.97.tar.gz
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cd Bio-Graphics-1.97
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perl Build.PL
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./Build
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./Build test
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sudo apt-get install libgd-tools
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./Build test
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sudo ./Build install
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</bash>
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=Install GBrowse=
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*Update [[GBrowse]] [[Glossary#CVS|cvs]] repository (it is an anonymous cvs checkout):
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  cd ~/software/gbrowse-pre-1.70/
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  cvs update -d
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  perl Makefile.PL
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  ... accept defaults
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  make
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  sudo make install
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=Tutorial=
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Go to http://localhost/gbrowse
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=GBrowse2=
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[[:Category:GBrowse 2|GBrowse 2]] is a re-architecture of [[GBrowse]] that uses [[Glossary#AJAX|AJAX]] techniques to allow independent rendering of tracks and multiple distributed databases.  It is designed to allow the use of load management and distributes processing on a compute farm, which enhanced performance and the user experience.  It is due to be released in late 2009.
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We will not cover GBrowse 2 in depth this year but will have a demo, time permitting.
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*[[Migrating_from_GBrowse_1.X_to_2.X|transitioning from GBrowse 1.x to 2.x]]
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*[[Running a GBrowse2 render farm]]
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*[[GBrowse 2.0 HOWTO]]
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=Example Advanced Features=
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==PrimerDesigner Plugin==
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[[Image:PrimerDesigner.png|right|border]]
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<span class="pops">[[GBrowse Plugins]]</span> allow you to add extra functionality to your genome browser.
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* The [[PrimerDesigner.pm|PrimerDesigner plugin]] used primer3 to design PCR primers for the selected region from within [[GBrowse]].
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* You can find out how to use and install this plugin, even see a ''fascinating'' video demonstration, <span class="pops">[[PrimerDesigner.pm|on the PrimerDesigner page]]</span>.
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==Rubber-Band Select Menus==
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[[Image:Rubber1.png|right|thumb|250px|An example of a select menu that appears after a region of the details panel is selected]]
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"Rubber-band", or drag-selection is a user-interface feature of [[GBrowse]] 1.69 and later. It a JavaScript/DHTML-based feature that works in all major web browsers and is turned on by default.
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* The rubber-band selection that is activating by dragging your mouse on the scalebar for the details section activated a menu that specifies various operations that can be performed on the selected sequence region.
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* The [[GBrowse Configuration HOWTO|GBrowse configuration file]] can be used to control the contents and appearance of this menu.
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* You can also add menus to the scalebar for the overview and regionview panels.
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* See [[RubberBandSelection]] for more information, including menus, configuration (and a video demo!).
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<br clear="all" />
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=Basic Chado Configuration (if we have time)=
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Normally, we'd need Bio::DB::Das::Chado, but it was installed for JBrowse yesterday.
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Starting material:
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  ~/software/gbrowse-pre-1.70/contrib/conf_files/07.chado.conf /etc/apache2/gbrowse.conf/
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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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==Materialized views for searching==
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Chado comes with a tool to materialize views written by developers at the SOL Genomics Network.  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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  gmod_materialized_view_tool.pl -c
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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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  all_feature_names
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  Where will this MV be located? (schemaname.tablename):
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  public.all_feature_names
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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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  y
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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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  weekly
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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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  feature_id integer,name varchar(255)
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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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  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
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  Enter a comma separated list of fields to index (or return for none):
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  feature_id,name
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  Enter the SQL queries for special indexes,
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; [[GBrowse NGS Tutorial]]
  or a file containing only the query (or return for none):
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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.
  create index all_feature_names_lower_name on all_feature_names (lower(name))
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  Enter 'y' to confirm, 'n' to re-enter data:
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; [http://youtu.be/jxA6VMN97Y8 GBrowse video tutorial]
  y
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: Produced by [http://eupathdb.org EuPathDB]; please direct praise and thanks to them!
  
 
[[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!