How to Set Up Visualizations in a Galaxy Instance

This page describes the administration steps needed to get Galaxy visualizations working.

Make sure your datatypes.conf is up to date

The file datatypes_conf.xml describes the data types (e.g. bed, wiggle) that Galaxy knows about and how to convert from one data type to another. datatypes_conf.xml must be up-to-date for visualizations to work.

If you haven't made changes to your datatypes_conf.xml file, you can simply copy the sample datatypes file to the active file:

cd <GALAXY_HOME_DIR>
cp datatypes_conf.xml.sample datatypes_conf.xml

If you've made changes to your datatypes_conf.xml file, the easiest approach is make a copy of datatypes_conf.xml.sample, add in your changes, and then copy your modified datatypes file to the active file:

cd <GALAXY_HOME_DIR>
cp datatypes_conf.xml.sample my_custom_datatypes_conf.xml
<customize my_custom_datatypes_conf.xml>
cp my_custom_datatypes_conf.xml datatypes_conf.xml

Install wigToBigWig, bedGraphToBigWig, and faToTwoBit from UCSC utilities

Galaxy visualizations require the UCSC utilities wigToBigWig, bedGraphToBigWig, and faToTwoBit to generate indices that are used for quickly searching data. Download these utilities from UCSC and add them to your (or your Galaxy user's) path.

Install BED tools

BEDtools are required for generating coverage data for aligned reads, intervals, and mutations. Download, compile, and add the bedtools executable (\<bedtools_dir>/bin) to your path.

Get genome chromosome length files

To visualize data for a genome build (e.g. hg19, mm10), visualization require the length of each chromosome in the build. Length files are named <build_name>.len and look like this:

chr1 27473282
chr2 38882233
...
chrX 28883322

Length files are stored in GALAXY_HOME_DIR/tool-data/shared/ucsc/chrom/ by default, but this location can be configured in the galaxy.ini file:

# Directory where chrom len files are kept, currently mainly used by trackster
#len_file_path = tool-data/shared/ucsc/chrom

For example, to visualize data on the hg18 build for humans, a file called hg18.len must exist in the len_file_path folder.

To download length files for all UCSC builds, run the following commands from your GALAXY_HOME directory:

cd <GALAXY_HOME_DIR>
mkdir ./tool-data/shared/ucsc/chrom/
python ./cron/build_chrom_db.py ./tool-data/shared/ucsc/chrom/

To display a build's genome data (i.e. bases/nucleotides) and differences between your data and the build, you will need to include the genome's data via the <GALAXY_HOME>/tool-data/twobit.loc configuration file. This file tells Galaxy where a build's twobit genome file is located and has the format (note the space between the columns is a character!):

<Build> <FullPathToFile>

An entry for the hg19 build might look like this:

hg19    /home/joe/galaxy/data/hg19/hg19.2bit

You can download twobit files for common genomes at UCSC by clicking on a build's 'Full data set' and downloading the build's twobit file. If you have a genome's fasta file, you can create a twobit file by using the UCSC utilties faToTwoBit tool.

NOTE: we're developing a graphical user interface for downloading and configuring builds in Galaxy. Stay tuned.

Restart your Instance

To ensure that all changes you made take effect, restart your Galaxy instance.