On Wed, May 1, 2013 at 4:23 AM, Cameron Jack cameron.jack@anu.edu.au wrote:
Dear Dev Team,
My program that I'm trying to integrate with Galaxy relies on SQLite databases to hold gene annotation information throughout multiple stages of processing. Given that the .db files produced by SQLite are not one of the standard data file types, is there any provision for a misc binary type for either a) data upload or b) intermediate processing? I find a lack of a misc 'binary' format surprising considering I can rename any file as .txt and it will upload as 'txt' format just fine (and presumably be loaded by my program within Galaxy just fine too).
There isn't a generic 'binary' datatype as far as I know, but I don't think it would be very useful. Other people have already tried defining their own SQLite3 datatype in Galaxy, but note that for Galaxy's workflows etc to work you must treat it as a write once, read many (WORM) file. http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-December/012302.html
I don't see anything using this in the Galaxy Tool Shed yet though (see the entry "Custom datatypes" on the left hand side of the Tool Shed): http://toolshed.g2.bx.psu.edu/
Similarly, my program produces image files (data plots) in any of the standard image file formats - PNG, PDF, JPEG. Would users be able to download these from Galaxy once my program has produced them?
Yes.
PDF is already covered by a core datatype, 'pdf'. JPEG is already covered by a core datatype, 'jpg'. PNG is already covered by a core datatype, 'png'
Peter