Kraken Data Table Definition is improper

[blankenberg]

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).

[blankenberg]

ping @davebx