Configuration options - Revision history

69.173.108.246: /* Configuring track order */

2013-11-18T19:38:49Z

Configuring track order

Thomas Admin: /* Configuring track aliases */

2013-11-15T22:23:21Z

Configuring track aliases

Thomas Admin: /* Configuring track visibility */

2013-11-15T22:23:00Z

Configuring track visibility

Thomas Admin: /* Configuring track aliases */

2013-11-15T22:22:30Z

Configuring track aliases

Thomas Admin: /* Configuring track visibility */

2013-11-15T22:22:09Z

Configuring track visibility

Thomas Admin: /* Configuring track order */

2013-11-15T22:21:52Z

Configuring track order

Thomas Admin at 21:52, 15 November 2013

2013-11-15T21:52:25Z

Thomas Admin at 21:41, 15 November 2013

2013-11-15T21:41:26Z

Thomas Admin at 21:38, 15 November 2013

2013-11-15T21:38:50Z

Thomas: Created page with "http://genomeview.org/content/configuration"

2013-09-03T14:39:10Z

Created page with "http://genomeview.org/content/configuration"

New page

http://genomeview.org/content/configuration

@@ Line 24: / Line 24: @@
 Some examples for remote files:
-  track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=100
+  <nowiki>track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=100</nowiki>
-  track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=200
+  <nowiki>track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=200</nowiki>

@@ Line 65: / Line 65: @@
 Some examples:
-  track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=Directional RNA-seq MCF 7
+  <nowiki>track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=Directional RNA-seq MCF 7</nowiki>
-  track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=Shorter (75) directional RNA-seq for MCF 10
+  <nowiki>track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=Shorter (75) directional RNA-seq for MCF 10</nowiki>
 Note: Track aliases are unrelated to aliases set up in the session file with the ALIAS command. You can make a track alias in a session file with the OPTION command:
   OPTION track:alias:gene=All the genes

@@ Line 48: / Line 48: @@
 Some examples:
-  track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=true
+  <nowiki>track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=true</nowiki>
- track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=false
+  <nowiki>track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=false</nowiki>
 ==Configuring track aliases==

@@ Line 57: / Line 57: @@
 For annotation features you give the type as XXX. For example:
-<code>
+ track:alias:gene=All the genes
-track:alias:gene=All the genes
+ track:alias:mRNA=MRNA track
-track:alias:mRNA=MRNA track
+ track:alias:CDS=Coding sequence features
 track:alias:CDS=Coding sequence features
 For any other data type, you have to specify the file file name or URL where the data resides.
 Some examples:
-<code>
+ track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=Directional RNA-seq MCF 7
-track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=Directional RNA-seq MCF 7
+ track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=Shorter (75) directional RNA-seq for MCF 10
 track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=Shorter (75) directional RNA-seq for MCF 10
 Note: Track aliases are unrelated to aliases set up in the session file with the ALIAS command. You can make a track alias in a session file with the OPTION command:
   OPTION track:alias:gene=All the genes

@@ Line 39: / Line 39: @@
 For annotation features you give the type as XXX. For example:
-<code>
-track:visible:gene=true
+ track:visible:gene=true
-track:visible:mRNA=false
+ track:visible:mRNA=false
-track:visible:CDS=true
+ track:visible:CDS=true
-</code>
 For any other data type, you have to specify the file file name or URL where the data resides.
 Some examples:
-<code>
+ track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=true
-track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=true
+ track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=false
 ==Configuring track aliases==

@@ Line 23: / Line 23: @@
 Some examples for remote files:
-<code>
-track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=100
+ track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=100
-track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=200
+ track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=200
-</code>
 This will also work with local files:
-<code>
+ track:weight:W:\thomas\rnaseq.bam=400
-track:weight:W:\thomas\rnaseq.bam=400
+ track:weight:W:\thomas\chipseq.bam=500
 track:weight:W:\thomas\chipseq.bam=500
 Deciding which method to use depends on the type of data: annotation are by type, other data is by file name.

@@ Line 9: / Line 9: @@
 </ul>
-The default configuration file is <a href="http://sourceforge.net/p/genomeview/code/HEAD/tree/genomeview/trunk/resources/conf/default.conf">available from the code repository</a>. This file is somewhat documented and can provide you some clues as which configuration options are available.
+The default configuration file is [http://sourceforge.net/p/genomeview/genomeview-code/ci/master/tree/resources/conf/default.conf available from the code repository] and should be considered the primary source of information regarding configuration options.
-<a name="trackorder"></a>
+== Configuring track order ==
 To configure the order of tracks you can use the <code>track:weight:XXX</code> configuration option. This will give a weight to each track and heavier tracks will be placed lower on the screen.
 For annotation features you have give the type as XXX. You cannot use the file name method below. For example:
 For any other data type, you have to specify the file file name or URL where the data resides. You cannot use the method described above.
@@ Line 40: / Line 37: @@
 Deciding which method to use depends on the type of data: annotation are by type, other data is by file name.
-<h2>Configuring track visibility</h2>
+== Configuring track visibility ==
 To configure the initial visibility of tracks you can use the <code>track:visible:XXX</code> configuration option. This will tell GenomeView whether the track is initially visible or hidden
@@ Line 57: / Line 54: @@
 track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=false
 </code>
-<a name="trackalias"></a>
-<h2>Configuring track aliases</h2>
+==Configuring track aliases==
 To change the name that appears next to each track to something that is more informative than the fully qualified path name, you can use the <code>track:alias:XXX=ALIAS</code> configuration option. This will tell GenomeView which name it should display
@@ Line 75: / Line 74: @@
 track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=Shorter (75) directional RNA-seq for MCF 10
 </code>

@@ Line 1: / Line 1: @@
 These pages discuss how to configure a number of things using the configuration file.
-There are three places from where GenomeView tries to load configuration information. It will look in the specified order.
+There are several places from where GenomeView tries to load configuration information. It will look in the specified order.
-<ol>
+<ul>
-<li>Configuration supplied on the command line with the --config option</li>
+<li>Config files specified in the session file</li>
 <li>Personal config file. This can be changed through the menu File -> Configuration.</li>
 <li>Default configuration present within the release package</li>
-</ol>
+</ul>
 The default configuration file is <a href="http://sourceforge.net/p/genomeview/code/HEAD/tree/genomeview/trunk/resources/conf/default.conf">available from the code repository</a>. This file is somewhat documented and can provide you some clues as which configuration options are available.

← Older revision		Revision as of 21:38, 15 November 2013
Line 1:		Line 1:
−	http://genomeview.org/~~content~~/configuration	+	These pages discuss how to configure a number of things using the configuration file.
		+
		+	There are three places from where GenomeView tries to load configuration information. It will look in the specified order.
		+	<ol>
		+	<li>Configuration supplied on the command line with the --config option</li>
		+	<li>Personal config file. This can be changed through the menu File -> Configuration.</li>
		+	<li>Default configuration present within the release package</li>
		+	</ol>
		+
		+	The default configuration file is <a href="http://sourceforge.net/p/genomeview/code/HEAD/tree/genomeview/trunk/resources/conf/default.conf">available from the code repository</a>. This file is somewhat documented and can provide you some clues as which configuration options are available.
		+
		+	<a name="trackorder"></a>
		+	<h2>Configuring track order</h2>
		+	To configure the order of tracks you can use the <code>track:weight:XXX</code> configuration option. This will give a weight to each track and heavier tracks will be placed lower on the screen.
		+
		+	For annotation features you have give the type as XXX. You cannot use the file name method below. For example:
		+	<code>
		+	track:weight:gene=1
		+	track:weight:mRNA=2
		+	track:weight:CDS=3
		+	</code>
		+
		+
		+	For any other data type, you have to specify the file file name or URL where the data resides. You cannot use the method described above.
		+
		+	Some examples for remote files:
		+	<code>
		+	track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=100
		+	track:weight:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=200
		+	</code>
		+
		+	This will also work with local files:
		+	<code>
		+	track:weight:W:\thomas\rnaseq.bam=400
		+	track:weight:W:\thomas\chipseq.bam=500
		+	</code>
		+	<a name="trackvisibility"></a>
		+
		+	Deciding which method to use depends on the type of data: annotation are by type, other data is by file name.
		+
		+	<h2>Configuring track visibility</h2>
		+	To configure the initial visibility of tracks you can use the <code>track:visible:XXX</code> configuration option. This will tell GenomeView whether the track is initially visible or hidden
		+
		+	For annotation features you give the type as XXX. For example:
		+	<code>
		+	track:visible:gene=true
		+	track:visible:mRNA=false
		+	track:visible:CDS=true
		+	</code>
		+
		+	For any other data type, you have to specify the file file name or URL where the data resides.
		+
		+	Some examples:
		+	<code>
		+	track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=true
		+	track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=false
		+	</code>
		+	<a name="trackalias"></a>
		+	<h2>Configuring track aliases</h2>
		+	To change the name that appears next to each track to something that is more informative than the fully qualified path name, you can use the <code>track:alias:XXX=ALIAS</code> configuration option. This will tell GenomeView which name it should display
		+
		+	For annotation features you give the type as XXX. For example:
		+	<code>
		+	track:alias:gene=All the genes
		+	track:alias:mRNA=MRNA track
		+	track:alias:CDS=Coding sequence features
		+	</code>
		+
		+	For any other data type, you have to specify the file file name or URL where the data resides.
		+
		+	Some examples:
		+	<code>
		+	track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF7_dir100.bam=Directional RNA-seq MCF 7
		+	track:alias:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=Shorter (75) directional RNA-seq for MCF 10
		+	</code>