How to Set Up Visualizations in a Galaxy Instance
This page describes the administration steps needed to get Galaxy visualizations working.
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
Galaxy visualizations require the UCSC utilities
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.
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.
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
# 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
To download length files for all UCSC builds, run the following commands from your
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
An entry for the hg19 build might look like this:
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
NOTE: we're developing a graphical user interface for downloading and configuring builds in Galaxy. Stay tuned.
To ensure that all changes you made take effect, restart your Galaxy instance.