Difference between revisions of "Configuration options"
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</ul> | </ul> | ||
| − | The default configuration file is | + | 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. |
| − | + | == Configuring track order == | |
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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. | 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 annotation features you have give the type as XXX. You cannot use the file name method below. For example: | ||
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| + | track:weight:gene=1 | ||
| + | track:weight:mRNA=2 | ||
| + | track:weight:CDS=3 | ||
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. | 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. | ||
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Deciding which method to use depends on the type of data: annotation are by type, other data is by file name. | Deciding which method to use depends on the type of data: annotation are by type, other data is by file name. | ||
| − | + | == 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 | 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 | ||
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track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=false | track:visible:http://www.broadinstitute.org/software/genomeview/demo/idea_challenge/Directional_RNAseq/MCF10_dir75.bam=false | ||
</code> | </code> | ||
| − | + | ||
| − | + | ==Configuring track aliases== | |
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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 | 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 | ||
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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 | ||
</code> | </code> | ||
| + | |||
| + | 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 | ||
Revision as of 23:52, 15 November 2013
These pages discuss how to configure a number of things using the configuration file.
There are several places from where GenomeView tries to load configuration information. It will look in the specified order.
- Config files specified in the session file
- Configuration supplied on the command line or start-up URLwith the --config option
- Personal config file. This can be changed through the menu File -> Configuration.
- Default configuration present within the release package
The default configuration file is available from the code repository and should be considered the primary source of information regarding configuration options.
Configuring track order
To configure the order of tracks you can use the track:weight:XXX 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:
track:weight:gene=1 track:weight:mRNA=2 track:weight:CDS=3
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:
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
This will also work with local files:
track:weight:W:\thomas\rnaseq.bam=400
track:weight:W:\thomas\chipseq.bam=500
<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.
Configuring track visibility
To configure the initial visibility of tracks you can use the track:visible:XXX 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:
track:visible:gene=true
track:visible:mRNA=false
track:visible:CDS=true
For any other data type, you have to specify the file file name or URL where the data resides.
Some examples:
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
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 track:alias:XXX=ALIAS configuration option. This will tell GenomeView which name it should display
For annotation features you give the type as XXX. For example:
track:alias:gene=All the genes
track:alias:mRNA=MRNA track
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:
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
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