GenomeView Manual - User contributions [en]

Supported versions

2017-11-28T16:17:02Z

Thomas Admin:

Currently available versions:

{|
! Version
! Webstart
! Applet*
! JavaScript embedding
! EOL
|-
| [http://genomeview.org/start/gvN36.jnlp N36(stable,webstart)]
| [[File:yes.png]]
| [[File:no.png]]
| [[File:no.png]]
| November 2018
|-
| [http://genomeview.org/start/gv2400.jnlp 2400 (stable,webstart)]
| [[File:yes.png]]
| [[File:no.png]]
| [[File:yes.png]]
| November 2014
|-
| [http://genomeview.org/start/gv2250.jnlp 2250]
| [[File:yes.png]]
| [[File:no.png]]
| [[File:no.png]]
| August 2014
|-
|[http://genomeview.org/start/gv2170.jnlp 2170 (experimental)]
| [[File:no.png]]
| [[File:no.png]]
| [[File:no.png]]
| --
|-
| [http://genomeview.org/start/gv2144.jnlp 2144]
| [[File:yes.png]]
| [[File:no.png]]
| [[File:yes.png]]
| May 2014
|-
| [http://genomeview.org/start/gv2126.jnlp 2126]
| [[File:yes.png]]
| [[File:no.png]]
| [[File:yes.png]]
| February 2014
|-
| [http://genomeview.org/gv2082.jnlp 2082 (experimental)]
| [[File:no.png]]
| [[File:no.png]]
| [[File:no.png]]
| --
|-
| [http://genomeview.org/start/gv2020.jnlp 2020]
| [[File:no.png]]
| [[File:no.png]]
| [[File:no.png]]
| Discontinued
|-
| [http://genomeview.org/start/gv1983.jnlp 1983]
| [[File:no.png]]
| [[File:no.png]]
| [[File:no.png]]
| Discontinued
|-
| [http://genomeview.org/start/gv1939.jnlp 1939]
| [[File:no.png]]
| [[File:no.png]]
| [[File:no.png]]
| Discontinued
|-
| [http://genomeview.org/start/gv1912.jnlp 1912]
| [[File:no.png]]
| [[File:no.png]]
| [[File:no.png]]
| Discontinued
|}

<table>
<tr><td>[[File:yes.png]]</td><td>Support offered on a best effort basis</td></tr>
<tr><td>[[File:no.png]]</td><td>Support offered on a low priority best effort basis</td></tr>
</table>

The developers of GenomeView offer a limited best-effort support for recent versions free of charge. Unfortunately, as this is a free product, we cannot guarantee anything. If you need a guaranteed service level agreement, [mailto:thomas@genomeview.org contact the project manager] and we will work out a solution.

We intend to provide one year support for newly released versions.

EOL: End of Life: After this data we cannot guarantee that this version will continue to run. Files may be archived from the server and so on.

If you need continued support for a particular feature or version past its EOL, you should [mailto:thomas@genomeview.org contact the project manager] for more information. We can work together to find a solution.

Note: Since March 2013, the support for the applet version has become a very low priority. There are too many platform/browser compatibility issues and we have too few resources to deal with all of them.

Talk:Command line options

2014-06-03T15:26:34Z

Thomas Admin: Blanked the page

Main Page

2014-06-03T15:16:13Z

Thomas Admin:

{{TOC|align=right}}

Welcome to the GenomeView manual. These pages aim to answer any questions you may have as an end-user, a platform-user or as a contributing developer.

This documentation is open for anyone to contribute to, just click the edit-button near the top and you can help make this a better resource for everyone. Due to increasing vandalism we were forced to shutdown anonymous editing and account sign-up. '''If you like an account, please drop a note to support@genomeview.org'''.

Feel free to copy documentation from the old manual to here, there are still some pages that need to be transferred and we're happy with any help you can spare.

== [[Quick start|Getting started with GenomeView in 5 minutes]] ==

<div style="float:left;width:49%">
{{Box-header|title=User manual}}
These manual pages describe how to use GenomeView and how to prepare your data to be usable in GenomeView.

[[Starting GenomeView]]

[[Preparing and loading data]] -- [[Preloaded data]]

[[Navigation]] -- [[Keyboard short-cuts]]

[[Visualizations]]

[[Search for...]]

[[Manipulating and configuring the views]]

[[Editing annotations]]

[[Exporting data and saving changes]]

[[More functionality with plugins]]

</div>
</div>

<div style="float:right;width:49%">
{{Box-header|title=Getting help}}

[[Frequently asked questions]]

[[I have a problem, help me, please]]

[[Report a bug or request a feature]]

[[Supported versions]]

</div>
</div>

<div style="clear:both;"></div>

<div style="float:left;width:49%">
{{Box-header|title=Platform-user manual}}
These manual pages describe how to integrate GenomeView with your web-based platform or how to communicate with GenomeView from 3-rd party software.

[[Using GenomeView from the command-line]]

[[Integration]]

[[Session files]] -- [[Configuration options]]

[[Communicating with GenomeView]]

[[Programming with GenomeView]]

[[Setting up authentication and encryption]]

[[Making a plugin]]

[[Integrating GenomeView as an editor]]

[[Setting up a Genome Explorer repository]]

</div>
</div>

<div style="float:right;width:49%">
{{Box-header|title=Developer manual}}
These pages are aimed towards contributors to GenomeView and developers who work directly on the GenomeView code.

Currently most of this documentation lives on [https://sourceforge.net/p/genomeview/wiki/ Sourceforge].

[[Unit test example data files]]

</div>
</div>
<div style="clear:both;"></div>

Main Page

2014-06-03T15:15:46Z

Thomas Admin:

{{TOC|align=right}}

Welcome to the GenomeView manual. These pages aim to answer any questions you may have as an end-user, a platform-user or as a contributing developer.

This documentation is open for anyone to contribute to, just click the edit-button near the top and you can help make this a better resource for everyone. '''Due to increasing vandalism we were forced to shutdown anonymous editing and account sign-up'''. If you like an account, please drop a note to support@genomeview.org.

Feel free to copy documentation from the old manual to here, there are still some pages that need to be transferred and we're happy with any help you can spare.

== [[Quick start|Getting started with GenomeView in 5 minutes]] ==

<div style="float:left;width:49%">
{{Box-header|title=User manual}}
These manual pages describe how to use GenomeView and how to prepare your data to be usable in GenomeView.

[[Starting GenomeView]]

[[Preparing and loading data]] -- [[Preloaded data]]

[[Navigation]] -- [[Keyboard short-cuts]]

[[Visualizations]]

[[Search for...]]

[[Manipulating and configuring the views]]

[[Editing annotations]]

[[Exporting data and saving changes]]

[[More functionality with plugins]]

</div>
</div>

<div style="float:right;width:49%">
{{Box-header|title=Getting help}}

[[Frequently asked questions]]

[[I have a problem, help me, please]]

[[Report a bug or request a feature]]

[[Supported versions]]

</div>
</div>

<div style="clear:both;"></div>

<div style="float:left;width:49%">
{{Box-header|title=Platform-user manual}}
These manual pages describe how to integrate GenomeView with your web-based platform or how to communicate with GenomeView from 3-rd party software.

[[Using GenomeView from the command-line]]

[[Integration]]

[[Session files]] -- [[Configuration options]]

[[Communicating with GenomeView]]

[[Programming with GenomeView]]

[[Setting up authentication and encryption]]

[[Making a plugin]]

[[Integrating GenomeView as an editor]]

[[Setting up a Genome Explorer repository]]

</div>
</div>

<div style="float:right;width:49%">
{{Box-header|title=Developer manual}}
These pages are aimed towards contributors to GenomeView and developers who work directly on the GenomeView code.

Currently most of this documentation lives on [https://sourceforge.net/p/genomeview/wiki/ Sourceforge].

[[Unit test example data files]]

</div>
</div>
<div style="clear:both;"></div>

Integration

2014-06-03T15:10:29Z

Thomas Admin: Undo revision 13006 by 151.252.42.26 (talk)

http://genomeview.org/content/integration

<i>Other topics that may be of interest: <a href="/content/integrating-genomeview-editor">Integrating as editor</a> and <a href="/content/communicating-genomeview">Communicating with GenomeView</a></i>

This page tries to explain how to integrate GenomeView in your website with your data. You can either make it available through Java Webstart, or as an applet. Whenever possible we recommend using Java Web
Start as it has better cross-platform and cross-browser support.

==General considerations==
To present your data in GenomeView optimally, there are a number of things you have to keep in mind.

===Indexing===
Please follow the recommendation in the [[recommended file formats]] page.

You will want to <a href="/content/preparing-fasta-files">index your reference sequence</a> to reduce loading times.

You may want to index annotation files, but this is not recommended unless they are over 10 Mb when compressed with gzip because you will loose structural information.

<p>To load an indexed file, you point GenomeView to the main file and GenomeView will try to find the index by itself.

===Compression===
<p>GenomeView supports GZIP compression transparently on all non-indexed file formats, i.e. compression and indexing are mutually exclusive. However as part of the indexing process, many file formats will be compressed.

<p><strong>Short read data</strong>
<p>Depending on what information you want to get out of the visualization, there are basically two ways to load short read data. The first one is the <a href="/content/short-read-track">Short Read Track</a> which will give you a detailed view with all individual reads. The second one is the <a href="/content/pile-track">Pile up track</a> which will give a more of a summary view/ coverage plot based on your sequence reads.

<p><a href="/content/preparing-short-read-alignments">Instructions to prepare data for the short read track</a>

<p><a href="/content/preparing-pileup">Instructions to prepare data for the pile up track</a>

==Present your data through a Java Web Start link==
The fastest and simplest way to get started and with integrating GenomeView with your data is by directly constructing a webstart link.

The default launch URL is located at http://genomeview.org/start/launch.jnlp. If you require a specific version, there are stable URLs available from the [[supported versions]] page.

The next step is constructing your URL to load sequence and features. Below a sample URL, which will load some sequence with annotation and some short reads. It will start with the [100000,200000] region visible.

<nowiki>http://genomeview.org/start/launch.jnlp?--position 100000:200000 --url http://www.broadinstitute.org/software/genomeview/demo/c_elegans/IV.fasta http://www.broadinstitute.org/software/genomeview/demo/c_elegans/IV.gff.gz http://www.broadinstitute.org/software/genomeview/demo/c_elegans/uwgs-rw_L2_FC6218_3.CHROMOSOME_IV.sorted.bam.bai</nowiki>

Pasting this URL in your browser will start GenomeView with data from C. elegans loaded.

[[Command line options]] to GenomeView can be added after the question mark after the installation URL.

The formalized version of the integration URL looks like this:

http://genomeview.org/start/launch.jnlp?[command line options for GenomeView separated with spaces]

'''Important:''' You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.

==Present your data through a Java Web Start session (recommended)==
A [[session file]] is a text file that contains instructions for GenomeView on which data to load and how to configure itself.

The basic set-up to start GenomeView with a [[session file]] is
<nowiki>http://genomeview.org/start/launch.jnlp?--session <URL to the session file></nowiki>

For example
[http://genomeview.org/start/launch.jnlp?--session%20http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php]

==Embedding GenomeView as an applet==
<div style="color:red">Support for the applet version of GenomeView is currently on hold due to ever changing Java support from the various browser and OS vendors. It is impossible to maintain any semblance of stability. All of the material below may or may not work.</div>

The key code that needs to be included in the body of your web page is:

<pre>
<script type="text/javascript" src="http://www.java.com/js/deployJava.js"></script>
<script type="text/javascript" src="http://genomeview.org/start/genomeview.js"></script>

<script type="text/javascript">
var gv_url = null;
var gv_config = 'http://genomeview.org/jsdemo/democonfig.txt';
var gv_extra = null;
var gv_location = null;
startGV(gv_url,gv_location,gv_config,gv_extra,500,400);
</script>
</pre>

<p>The <code>gv_url</code> can be used to pre-load a reference sequence. This file will be loaded first and only then will GenomeView proceed with loading additional data.

<p>The configuration file you want to use, can be specified using the <code>gv_config</code> option.

<p>All other data that you want to have loaded can be specified in a space separated list in <code>gv_extra</code>. These data sets will be loaded in parallel.

<p>The location that will initially be visible, can be set by <code>gv_location</code>. The position is in the format <entry>:<start position>:<end position> The entry part is optional can be omitted in which case it becomes <start position>:<end position>

<p><em>Note: we strongly recommend you use the genomeview.js we provide as that's the one we keep up to date with progressing releases.</em>

Integration

2014-06-03T15:10:10Z

Thomas Admin: Undo revision 13007 by 134.91.140.76 (talk)

http://genomeview.org/content/integration

<i>Other topics that may be of interest: <a href="/content/integrating-genomeview-editor">Integrating as editor</a> and <a href="/content/communicating-genomeview">Communicating with GenomeView</a></i>

This page tries to explain how to integrate GenomeView in your website with your data. You can either make it available through Java Webstart, or as an applet. Whenever possible we recommend using Java Web
Start as it has better cross-platform and cross-browser support.

I loved your blog article. Really Cool. aaccddgedddgdaek

==Present your data through a Java Web Start link==
The fastest and simplest way to get started and with integrating GenomeView with your data is by directly constructing a webstart link.

The default launch URL is located at http://genomeview.org/start/launch.jnlp. If you require a specific version, there are stable URLs available from the [[supported versions]] page.

The next step is constructing your URL to load sequence and features. Below a sample URL, which will load some sequence with annotation and some short reads. It will start with the [100000,200000] region visible.

<nowiki>http://genomeview.org/start/launch.jnlp?--position 100000:200000 --url http://www.broadinstitute.org/software/genomeview/demo/c_elegans/IV.fasta http://www.broadinstitute.org/software/genomeview/demo/c_elegans/IV.gff.gz http://www.broadinstitute.org/software/genomeview/demo/c_elegans/uwgs-rw_L2_FC6218_3.CHROMOSOME_IV.sorted.bam.bai</nowiki>

Pasting this URL in your browser will start GenomeView with data from C. elegans loaded.

[[Command line options]] to GenomeView can be added after the question mark after the installation URL.

The formalized version of the integration URL looks like this:

http://genomeview.org/start/launch.jnlp?[command line options for GenomeView separated with spaces]

'''Important:''' You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.

==Present your data through a Java Web Start session (recommended)==
A [[session file]] is a text file that contains instructions for GenomeView on which data to load and how to configure itself.

The basic set-up to start GenomeView with a [[session file]] is
<nowiki>http://genomeview.org/start/launch.jnlp?--session <URL to the session file></nowiki>

For example
[http://genomeview.org/start/launch.jnlp?--session%20http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php]

==Embedding GenomeView as an applet==
<div style="color:red">Support for the applet version of GenomeView is currently on hold due to ever changing Java support from the various browser and OS vendors. It is impossible to maintain any semblance of stability. All of the material below may or may not work.</div>

The key code that needs to be included in the body of your web page is:

<pre>
<script type="text/javascript" src="http://www.java.com/js/deployJava.js"></script>
<script type="text/javascript" src="http://genomeview.org/start/genomeview.js"></script>

<script type="text/javascript">
var gv_url = null;
var gv_config = 'http://genomeview.org/jsdemo/democonfig.txt';
var gv_extra = null;
var gv_location = null;
startGV(gv_url,gv_location,gv_config,gv_extra,500,400);
</script>
</pre>

<p>The <code>gv_url</code> can be used to pre-load a reference sequence. This file will be loaded first and only then will GenomeView proceed with loading additional data.

<p>The configuration file you want to use, can be specified using the <code>gv_config</code> option.

<p>All other data that you want to have loaded can be specified in a space separated list in <code>gv_extra</code>. These data sets will be loaded in parallel.

<p>The location that will initially be visible, can be set by <code>gv_location</code>. The position is in the format <entry>:<start position>:<end position> The entry part is optional can be omitted in which case it becomes <start position>:<end position>

<p><em>Note: we strongly recommend you use the genomeview.js we provide as that's the one we keep up to date with progressing releases.</em>

Integration

2014-06-03T15:09:58Z

Thomas Admin: Undo revision 13008 by 118.174.199.77 (talk)

Integration

2014-06-03T15:09:44Z

Thomas Admin: Undo revision 13010 by 78.38.101.2 (talk)

Integration

2014-06-03T15:09:08Z

Thomas Admin: Reverted edits by Thomas Admin (talk) to last revision by 78.38.101.2

2013-11-15T22:55:53Z

Thomas Admin: /* Repository file format */

Setting up a Genome Explorer repository

2013-11-15T22:55:00Z

Thomas Admin: /* Repository file format */

Setting up a Genome Explorer repository

2013-11-15T22:54:34Z

Thomas Admin: /* Repository file format */

Setting up a Genome Explorer repository

2013-11-15T22:54:01Z

Thomas Admin: /* Repository file format */

2013-11-15T21:01:57Z

Thomas Admin: /* Body */

Session files allow you to organize a large number of data files and config options in a single file.

An example session file:
http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php

You can use 'View source', or something similar, in your browser to see the actual file structure. It is a plain text file with on each line a file that needs to be loaded.

==File structure ==

===Header===
Make sure the file starts with a line that contains the words 'GenomeView' and 'session'. These two words have to be on the first line!

We recommend:
##GenomeView session

This header is used to detect the file format by GenomeView.

=== Body ===

The remainder of the file contains lines that have various instructions to load data, configure GenomeView or load plugins. The table below has an overview of all options.

{|
!Instruction*
!Value
|-
|CONFIG
|URL or local file path to the configuration file. This line should be the first in the session file, otherwise some data may not have the correct configuration file when initializing.
|-
|DATA**
|URL or local file path for a data file. This file will be loaded. You do not need to specify the index, GenomeView will look for it in the same folder.
|-
|PREFIX
|URL or local file path prefix. The value of this instructions will be prepended to any DATA or CONFIG pairs that follow this instruction. A PREFIX values is only valid for subsequent DATA and CONFIG pairs. This can to simplify loading many files from multiple locations. To reset the PREFIX, you can use an empty value.
|-
|OPTION
|Key=value definition of a single configuration option. This is suited to override a few config options as needed.
|-
|ALIAS [primary name]=[display name].
|Add an additional synonym for an Entry (chromosome). This can be useful if your data has different identifiers for the same sequence in different files. The primary name will be used to connect the data types. Multiple primary names can point to the display name, in that case you can use the aliases to connect multiple different IDs.
|-
|LOCATION
|Set the visible location to the specified location. The location needs to be specified [entry]:[start position]-[end position].
|-
|PLUGIN
|Allows you to request the user to automatically install a plugin. The plugin needs to be specified as a URL to the zip file. You can use relative names in conjunction with the PREFIX parameter
|}

** The legacy keywords C, U and F will continue to work.

Each of the lines should be organized like this:
instruction[tab, colon or space]value

For example, all of these are valid ways to specify a file
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/annotation.gff
DATA:http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/operon.gff

Important: You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.

===Example session file===

##GenomeView session -- DO NOT DELETE THIS LINE
CONFIG http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/tbconfig.txt
ALIAS MT_H37RV_V2=MyTBGenome
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/annotation.gff
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/operon.gff
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/sRNA.gff
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/rRNA.gff
PLUGIN http://www.broadinstitute.org/software/genomeview/resources/save2pdf-1.1.zip

== Starting a session with a launch URL ==
The basic set-up to start GenomeView with a [[session file]] is
<nowiki>http://genomeview.org/start/launch.jnlp?--session <URL to the session file></nowiki>

For example
[http://genomeview.org/start/launch.jnlp?--session%20http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php]

== Hiding the session URL ==
Typically you don't even have to expose this URL and you can use a simple PHP script index.php that redirects to that location.
For example:
<nowiki>header("Location: http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php");</nowiki>