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Admin/DataIntegration

Data Integration for Local Instances

Please note that "built-in" or "cached" data can now be managed directly from within the Galaxy admin interface. For details, see: Data Managers

Built-in data files are critical for many Galaxy tools. This page will describe how to get data into your local instance of Galaxy in a general way. For instructions specific for organizing and indexing data for use with tools, see Data Preparation. Additional instructions are available for reviewing or retrieving the exact data hosted on the public Main instance or for performing more complex data prep used by specific tool groups.

How it works

There are several steps needed for adding a genome to Galaxy. The first is to get the actual data needed and to put it into an appropriate directory accessible to the Galaxy instance. Then you need to establish the particular .loc ("location") file. Finally, make sure that the genome is referenced in the $GALAXYROOT/tool-data/shared/ucsc/builds.txt file.

Note that as of early 2014, more than a builds.txt file change is needed to establish a new reference genome. If not using Data Managers, you must make the necessary changes/additions to the new Data Tables or use the alternative configuration file (described on that same Data Tables wiki, near the end).

Get the data

First you need to determine what type of data you need. Usually these are .fasta, .nib, .2bit, or special index files, but each tool has a specific need. Open up the XML for the particular tool and identify the .loc file referred to in either a validator tag or options tag. Open the $GALAXYROOT/tool-data/<filename>.loc.sample file, and read it to discover the type of files necessary. Once you know what you need, you can go acquire it.

There are several ways to get the data. If you don't already have the right file on your system, you will need to get it from a site such as UCSC.

Or, if you would like to obtain the data as available on the public Galaxy Main instance, these can retrieved from the rsync server. Read more here: Rsync

Set up the loc file

The .loc.sample files themselves include instructions for setting them up. In all cases, there is one reference genome per line, with tab-separated information. Create the needed .loc files, add your sequence and index data, and place these into the $GALAXYROOT/tool-data directory. This can be modified, but is the default location configured in config/galaxy.ini and the other configuration files referenced by it, in this section:

# -- Files and directories

# Path where genome builds are stored. This defaults to tool-data/genome
#genome_data_path = tool-data/genome

...<skipped>...

# XML config file that contains data table entries for the ToolDataTableManager. This file is manually
# maintained by the Galaxy administrator.
#tool_data_table_config_path = tool_data_table_conf.xml

# XML config file that contains additional data table entries for the ToolDataTableManager.  This file
# is automatically generated based on the current installed tool shed repositories that contain valid
# tool_data_table_conf.xml.sample files.  At the time of installation, these entries are automatically
# added to the following file, which is parsed and applied to the ToolDataTableManager at server start up.
#shed_tool_data_table_config = shed_tool_data_table_conf.xml

*.loc file examples

With tabs separating the information:

alignseq.loc

align	anoGam1	dm1	/depot/data2/galaxy/anoGam1/align/dm1
align	anoGam1	dm2	/depot/data2/galaxy/anoGam1/align/dm2
align	canFam1	hg17	/depot/data2/galaxy/canFam1/align/hg17

bowtie2_indexes.loc

hg38canon  hg38      Human (Homo sapiens) (b38): hg38 Canonical	   /galaxy/data/hg38/hg38canon/bowtie2_index/hg38canon
hg38	   hg38	     Human (Homo sapiens) (b38): hg38	           /galaxy/data/hg38/hg38full/bowtie2_index/hg38full
dipOrd1	   dipOrd1   Kangaroo rat (Dipodomys ordii): dipOrd1	   /galaxy/data/dipOrd1/bowtie2_index/dipOrd1
braFlo1	   braFlo1   Lancelet (Branchiostoma floridae): braFlo1	   /galaxy/data/braFlo1/bowtie2_index/braFlo1
anoCar1	   anoCar1   Lizard (Anolis carolinensis): anoCar1	   /galaxy/data/anoCar1/bowtie2_index/anoCar1
anoCar2	   anoCar2   Lizard (Anolis carolinensis): anoCar2	   /galaxy/data/anoCar2/bowtie2_index/anoCar2

Also see the Rsync wiki if you want to obtain the exact same location files used on http://usegalaxy.org for full size examples or for use as base-line files when configuring your own server.

Add new genome as Galaxy build

Final and most important item needed is to include any new reference genomes in the builds.txt file. This is the list of reference genomes appear in the Genome or Database/Build search box when you upload a file or change a file's metadata (Where to find these? See the Rsync link directly above for screenshots).

To modify the builds.txt file, add a line to $GALAXYROOT/tool-data/shared/ucsc/builds.txt for your genome. The format of this line can vary, but should contain enough information to uniquely identify the genome, the source, any external build nomenclature, and the dbkey selected for use within your Galaxy instance. See the public Main server for examples: http://usegalaxy.org

Restart the server

Any time you change data information, the server has to be restarted!!!