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.
- Review or retrieve usegalaxy.org reference genomes, indexes, and loc files by rsync: Usegalaxy.org Rsync
- "Fetch Alignment" tools data prep: Reference MAFs
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.
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:
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
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
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!!!