Difference between revisions of "JBrowse"
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| − | + | __NOTITLE__ | |
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| − | + | [[File:JBrowseLogo.png|center|400px|alt=JBrowse logo]] | |
| − | = | + | <div class="componentBox"> |
| + | <div class="compBoxHdr">Status</div> | ||
| + | *mature release | ||
| + | *active development | ||
| + | *active support | ||
| + | <div class="compBoxHdr">Resources</div> | ||
| + | *[http://jbrowse.org Home page] | ||
| + | *[http://jbrowse.org/install/ Download] | ||
| + | {{ComponentBoxSectionHeader | Events}} | ||
| + | {{SchoolBoxItem|JBrowse}} | ||
| + | </div> | ||
| − | + | ==About JBrowse== | |
| − | + | JBrowse is a genome browser with a fully dynamic AJAX interface, being developed as the eventual successor to GBrowse. It is very fast and scales well to large datasets. JBrowse does almost all of its work directly in the user's web browser, with minimal requirements for the server. | |
| − | + | Visit the [http://jbrowse.org JBrowse website]. | |
| − | = | + | ==Downloads== |
| − | + | Download JBrowse: [http://jbrowse.org/install/ http://jbrowse.org/install/] | |
| − | + | The source code for JBrowse can be downloaded from http://github.com/GMOD/jbrowse. | |
| − | + | ==Using JBrowse== | |
| − | + | ||
| − | + | The [http://jbrowse.org/code/latest-release/docs/tutorial/ Getting Started with JBrowse Tutorial] provides a basic step-by-step recipe for quickly getting up and running with JBrowse. | |
| − | + | ===System Requirements=== | |
| + | |||
| + | For a full JBrowse installation, including support for WIG and BAM data, your system must have: | ||
* a working internet connection for downloading Perl modules from CPAN | * a working internet connection for downloading Perl modules from CPAN | ||
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For tips on installing these baseline libraries, see [[JBrowse Troubleshooting]]. | For tips on installing these baseline libraries, see [[JBrowse Troubleshooting]]. | ||
| − | + | ===Installation=== | |
| − | + | ||
| − | + | 1. [http://jbrowse.org/install/ Download JBrowse] onto your web server. | |
| + | |||
| + | 2. Unpack JBrowse into a directory that is served by your web browser. On many systems, this defaults to <code>/var/www</code>. | ||
| + | |||
| + | cd /var/www | ||
| + | tar -xzf jbrowse-*.tar.gz | ||
| + | |||
| + | '''Make sure you have permissions to write to the contents of the jbrowse/ directory you have just created.''' | ||
| + | |||
| + | 3. Run the automated-setup script, <code>./setup.sh</code>, which will attempt to install all of JBrowse's (modest) prerequisites for you in the <code>jbrowse/</code> directory itself. <code>setup.sh</code> does not need to be run as root or with <code>sudo</code>. | ||
| + | |||
| + | 4. When you can see the included Volvox example data, you are ready to configure JBrowse to show your own data! | ||
| + | |||
| + | ===Configuration=== | ||
| − | + | See the [[JBrowse Configuration Guide]] for information on: | |
| − | + | * [[JBrowse Configuration Guide#Reference Sequences|Formatting reference sequences]] (e.g. from FASTA files, or a Chado database) | |
| − | + | * [[JBrowse Configuration Guide#Feature Tracks|Feature Tracks]] (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser) | |
| − | + | * [[JBrowse Configuration Guide#Image Tracks|Image Tracks]] (e.g. from WIG files) | |
| − | + | * [[JBrowse Configuration Guide#Wiggle_Tracks|Wiggle/BigWig Tracks]] | |
| − | + | * [[JBrowse Configuration Guide#Name_Searching_and_Autocompletion | Name Search and Autocompletion]] | |
| − | + | * [[JBrowse Configuration Guide#Removing Tracks|Removing tracks]] | |
| − | + | * [[JBrowse Configuration Guide#Compressing data on the server|Compressing data stored on the server]] | |
| − | + | * [[JBrowse Configuration Guide#URL Control | URL control ]] | |
| − | + | * [[JBrowse Configuration Guide#Faceted Track Selection | Faceted track selection ]] | |
| − | + | * [[JBrowse Configuration Guide#Anonymous Usage Statistics | Anonymous usage statistics ]] | |
| − | + | Additional topics: | |
| − | + | * [[JBrowseDev/Using Configuration Files With JBrowse|Using Configuration Files with biodb-to-json.pl]] | |
| − | + | * [[JBrowseDev/Using a Database With JBrowse|Using an Existing Database with JBrowse]] | |
| − | = | + | ===Documentation=== |
For data format specifications, developer information, and so forth, see [[JBrowse Advanced Topics]]. | For data format specifications, developer information, and so forth, see [[JBrowse Advanced Topics]]. | ||
| − | = | + | ==Publications, Tutorials, and Presentations== |
| − | |||
| − | = | + | |
| + | ===Presentations=== | ||
| + | |||
| + | * April 2012 - GMOD 2012 Community Meeting, Robert Buels: [[Media:RBuels_JBrowse_apr2012.pdf|PDF]] | ||
| + | * January 2012 - Plant and Animal Genome (PAG) XX: [[Media:Rbuels_jbrowse_pag2012.pdf|PDF]] | ||
| + | * April 2010 - UCSC genome browser group ("genecats") meeting: [[Media:JBrowse-UCSC-4-21-10.pdf|PDF]] | ||
| + | * August 2009 - [[August 2009 GMOD Meeting|GMOD Community Meeting]]: [[ August 2009 GMOD Meeting#JBrowse | Talk summary ]] | ||
| + | |||
| + | ==Contacts and Mailing Lists== | ||
Please direct questions and inquiries regarding JBrowse to the mailing lists below. | Please direct questions and inquiries regarding JBrowse to the mailing lists below. | ||
| − | '' | + | ''Requests for help should be directed to [mailto:gmod-ajax@lists.sourceforge.net gmod-ajax@lists.sourceforge.net].''' |
| + | |||
| + | {| class="wikitable" | ||
| + | | | ||
| + | ! Mailing List Link | ||
| + | ! Description | ||
| + | ! Archive(s) | ||
| + | [[:Template:MailingListsJBrowse]] | ||
| + | |} | ||
| − | |||
| − | = JBrowse Development = | + | ==JBrowse Development== |
JBrowse is an open-source project, started and managed by the laboratory of '''[mailto:ihh@berkeley.edu Ian Holmes]''' at the [http://berkeley.edu University of California, Berkeley]. | JBrowse is an open-source project, started and managed by the laboratory of '''[mailto:ihh@berkeley.edu Ian Holmes]''' at the [http://berkeley.edu University of California, Berkeley]. | ||
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As of January 2012, the lead developer of JBrowse is [[User:RobertBuels|Robert Buels]]. Most of JBrowse was originally written by [mailto:mitch_skinner@berkeley.edu Mitch Skinner]. | As of January 2012, the lead developer of JBrowse is [[User:RobertBuels|Robert Buels]]. Most of JBrowse was originally written by [mailto:mitch_skinner@berkeley.edu Mitch Skinner]. | ||
| − | There is a [[#Mailing Lists|mailing list for developers]], and there is usually a teleconference on the 3rd Monday of the month at 2pm Pacific US time. We welcome participation from Please contact [[User:RobertBuels|Robert Buels]] if you would like to listen in or participate. | + | There is a [[#Mailing Lists|mailing list for developers]], and there is usually a teleconference on the 3rd Monday of the month at 2pm Pacific US time. We welcome participation from anyone and everyone. Please contact [[User:RobertBuels|Robert Buels]] if you would like to listen in or participate. |
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| − | + | ==More on JBrowse== | |
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| − | + | See [[:Category:JBrowse]] | |
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| − | + | <references /> | |
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[[Category:GMOD Components]] | [[Category:GMOD Components]] | ||
[[Category:AJAX]] | [[Category:AJAX]] | ||
[[Category:JBrowse]] | [[Category:JBrowse]] | ||
Revision as of 19:19, 24 August 2012
__NOTITLE__
Contents
About JBrowse
JBrowse is a genome browser with a fully dynamic AJAX interface, being developed as the eventual successor to GBrowse. It is very fast and scales well to large datasets. JBrowse does almost all of its work directly in the user's web browser, with minimal requirements for the server.
Visit the JBrowse website.
Downloads
Download JBrowse: http://jbrowse.org/install/
The source code for JBrowse can be downloaded from http://github.com/GMOD/jbrowse.
Using JBrowse
The Getting Started with JBrowse Tutorial provides a basic step-by-step recipe for quickly getting up and running with JBrowse.
System Requirements
For a full JBrowse installation, including support for WIG and BAM data, your system must have:
- a working internet connection for downloading Perl modules from CPAN
- compilers for C and C++
-
make - the
svnSubversion client (for fetching thesamtoolscode, needed for BAM support) - development libraries and header files (not just compiled shared objects) for:
- libpng
- Zlib
- GD
For tips on installing these baseline libraries, see JBrowse Troubleshooting.
Installation
1. Download JBrowse onto your web server.
2. Unpack JBrowse into a directory that is served by your web browser. On many systems, this defaults to /var/www.
cd /var/www tar -xzf jbrowse-*.tar.gz
Make sure you have permissions to write to the contents of the jbrowse/ directory you have just created.
3. Run the automated-setup script, ./setup.sh, which will attempt to install all of JBrowse's (modest) prerequisites for you in the jbrowse/ directory itself. setup.sh does not need to be run as root or with sudo.
4. When you can see the included Volvox example data, you are ready to configure JBrowse to show your own data!
Configuration
See the JBrowse Configuration Guide for information on:
- Formatting reference sequences (e.g. from FASTA files, or a Chado database)
- Feature Tracks (e.g. from BED or GFF files, a Chado database, or the UCSC genome browser)
- Image Tracks (e.g. from WIG files)
- Wiggle/BigWig Tracks
- Name Search and Autocompletion
- Removing tracks
- Compressing data stored on the server
- URL control
- Faceted track selection
- Anonymous usage statistics
Additional topics:
Documentation
For data format specifications, developer information, and so forth, see JBrowse Advanced Topics.
Publications, Tutorials, and Presentations
Presentations
- April 2012 - GMOD 2012 Community Meeting, Robert Buels: PDF
- January 2012 - Plant and Animal Genome (PAG) XX: PDF
- April 2010 - UCSC genome browser group ("genecats") meeting: PDF
- August 2009 - GMOD Community Meeting: Talk summary
Contacts and Mailing Lists
Please direct questions and inquiries regarding JBrowse to the mailing lists below.
Requests for help should be directed to gmod-ajax@lists.sourceforge.net.'
| Mailing List Link | Description | Archive(s) |
|---|
JBrowse Development
JBrowse is an open-source project, started and managed by the laboratory of Ian Holmes at the University of California, Berkeley.
The JBrowse source code repository is kept on GitHub. Please feel very free to fork the code on GitHub and make modifications and improvements, submitting pull requests. GitHub has a very nice tutorial on how to get started with this style of development.
As of January 2012, the lead developer of JBrowse is Robert Buels. Most of JBrowse was originally written by Mitch Skinner.
There is a mailing list for developers, and there is usually a teleconference on the 3rd Monday of the month at 2pm Pacific US time. We welcome participation from anyone and everyone. Please contact Robert Buels if you would like to listen in or participate.
More on JBrowse
See Category:JBrowse
