Hi list,

The tool I am currently wrapping has built-in data, which may be used by the tool users (through a relevant <from_data_table> + .LOC file configuration).
They are .fasta databases which are rather small and are thus bundled in the tool distribution package.

Thanks to the tool_dependencies.xml file, said distribution package is downloaded at install time, code is compiled, and since they are here, the data files are copied to $INSTALL_DIR too, ready to be used.

After that, the user still has to edit tool-data/my_fancy_data_files.loc ; but the thing is, during the install I know where these data files are (since I copied those there), so I would like to save the user the trouble and set up this file automagically.

I would have two questions:

1/ Is it okay to have tool built-in data files in $INSTALL_DIR, or would it be considered bad practice?

2/ Is there a way to set up the tool-data/my_fancy_data_files.loc during the install? Here are the options I though of:
*shipping a “real” my_fancy_data_files.loc.sample with the good paths already set-up, which is going to be copied as the .loc file (a rather ugly hack)
*using more <action type="shell_command"> during install to create my_fancy_data_files.loc (but deploying this file it is not part of the tool dependency install per se)
*variant of the previous : shipping my_fancy_data_files.loc as part of the tool distribution package, and copy it through shell_command (same concern than above).

Any thoughts?

Cheers,

--
Jean-Frédéric
Bonsai Bioinformatics group