Tae-Hoon Have a look at this wiki page: http://bitbucket.org/galaxy/galaxy-central/wiki/AddingDatatypes well, you can always delegate this to the script you are going to execute within galaxy. As long as the user 'galaxy' has access to the this folder which (I assume) is outside the galaxy directory. It might need some hard coding of the path in your script, and then do something like, pseudo code: - read contents of directory - if file present run your tool And this can all be based on parameters (ie: which directory, which file name ) you provide (or ask for) via the interface. Maybe you should provide more details about the task you want to do with galaxy and the someone might be able to help you in a more specific way. Hans