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bernt-matthias committed Mar 6, 2024
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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 to separate tool data of shed installed tools by setting (`shed_tool_data_path`).
It's possible to separate tool data of ToolShed-installed tools by setting `shed_tool_data_path`.

Tool data consists of:

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In order to make tool data usable from Galaxy tools so called `loc` files are used.
Those are tabular (by default tab separated) files with the extension `.loc`.
Besides the actual paths the entries can contain, e.g. IDs, names, or other metadata
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
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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 thus is `tool-data/toolshed.g2.bx.psu.edu/`. Note that
these directories will also contain tool data config files, but they are unused.
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.

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