galaxyproject / galaxyproject/tools-devteam
Kraken Data Table Definition is improper
- Dominant language
- Python
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Description
See: https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/tool_data_table_conf.xml.sample
and usage in https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/kraken.xml
```
bacteria_greengenes_rdp Bacteria_GreenGenes_RDP /path/to/data/kraken_database/bacteria_greengenes_rdp
```
Here, we have 3 columns defined `value, name, path`, where `value` is only ever used internally in Galaxy (good for value), but the `name` and `path` must correspond to actual directories on disk, where `path` is a subdir of `name`.
The `name` should actually be a better human readable description/name (able to include any printable character).
A quick glance at http://ccb.jhu.edu/software/kraken/MANUAL.html, indicates that we shouldn't even need to use `path` for the env var `$KRAKEN_DB_PATH` that is currently being done:
`Note that the KRAKEN_DB_PATH directory list can be skipped by the use of any absolute (beginning with /) or relative pathname (including at least one /) as the database name.`
`path` should be the path to the kraken db (including at least one `/`, so the current directory setup is fine), and `name` should be a human readable description that can include all kinds of characters (spaces, question marks, parenthesis, etc).
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