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Tool data

Galaxy stores tool data in the path defined by tool_data_path (by default tool-data/). It’s possible to separate tool data of toolshed-installed tools by setting shed_tool_data_path.

Tool data consists of:

  1. the actual data

  2. one or more loc files

  3. entries in a tool data table (config) file

History

In order to understand the naming and structure of these three components it might be of advantage to look in the history. Tool data was organized in tabular loc that contained metadata and paths of the data. Those files were installed with the tool and could be accessed with the from_file mechanism from tools. Since each tool version had it’s own loc file the maintenance was difficult. With tool data tables an additional abstraction layer was introduced that is used from tools via from_datatable.

Tool data

This is the actual data that is stored by default in tool_data_path. It may be favorable to store the actual tool data in a separate folder. For manually managed tool data this can be achieved by simply storing the data in another folder. For data that is added by data managers this can be achieved by setting galaxy_data_manager_data_path.

loc files

In order to make tool data usable from Galaxy tools loc files are used. Those are tabular (by default tab separated) files with the extension .loc. Besides the actual paths, the entries can contain IDs, names, or other metadata that can be used in tools to select reference data. The paths should be given as absolute paths, but can also be given relative to the Galaxy root dir. By default loc files are installed in tool_data_path (where also built-in loc files are stored). By setting shed_tool_data_path this can be separated.

Tool data tables

The tool data tables that should be used in a Galaxy instance are listed in tool data table config files. In addition these contain metadata.

Tool data table config files are XML files listing tool data table configurations:

<tables>
    ....
</tables>

An entry for a tool data looks like this

<table name="bwa_indexes_color" comment_char="#" allow_duplicate_entries="False">
    <columns>value, dbkey, name, path</columns>
    <file path="bwa_index_color.loc" />
</table>

  • table: name, comment_char (default "#"), separator (default "\t"), allow_duplicate_entries (default True), empty_field_value (default "")

  • columns: a comma separated list of column names

  • file: path (alternatively url, from_config)

Tool data table entries for tools installed from a toolshed have an additional element tool_shed_repository and sub-tags tool_shed repository_name, repository_owner, installed_changeset_revision, e.g.:

<table name="plasmidfinder_database" comment_char="#">
    <columns>value, name, date, path</columns>
    <file path="/home/berntm/projects/galaxy/tool-data/toolshed.g2.bx.psu.edu/repos/iuc/plasmidfinder/7075b7a5441b/plasmidfinder_database.loc.sample"/>
    <tool_shed_repository>
        <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
        <repository_name>plasmidfinder</repository_name>
        <repository_owner>iuc</repository_owner>
        <installed_changeset_revision>7075b7a5441b</installed_changeset_revision>
    </tool_shed_repository>
</table>

The file path points to a loc file and can be given relative (to the tool_data_path) or absolute. If a given relative path does not exist also the base name is checked (many tools use something like tool-data/xyz.loc and store example loc files in a tool-data/ directory in the tool repository). Currently also .loc.sample may be used in case the specified .loc is absent.

Galaxy uses two tool data table config files:

  • tool_data_table_config_path: by default tool_data_table_conf.xml in Galaxy’s config/ directory.

  • shed_tool_data_table_config: by default shed_tool_data_table_conf.xml in Galaxy’s config/ directory. This file lists all tool data tables of tools installed from a toolshed. Note that the entries are versioned, i.e. there is a separate entry for each tool and tool version.

The tool data table config files can (and do) contain multiple entries for the same data table (identified by the same name). These content of the corresponding loc files are merged when they are loaded.

When a new tool is installed that uses a data table a new entry is added to shed_tool_data_table_config and a loc file is placed in a versioned subdirectory in tool_data_path (in a subdirectory that has the name of the toolshed). By default this is tool-data/toolshed.g2.bx.psu.edu/. Note that these directories will also contain tool data table config files, but they are unused.