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 $INSTAL L_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 $INSTAL L_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 

Any thoughts? 


Bonsai Bioinformatics group
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