Configuration options

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 <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.

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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 <a name="trackalias"></a>

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