There is a problem with the 0.5 bx-python build used in Galaxy (that i think has been fixed in 0.6) can you please update the central repository to include 0.6 ASAP please? Basically, if you try to run maf join (or other functions maf tools) and select a genome that is not present in the first block, you will get an empty file returned. It seems from the descriptions on James' site that this may be fixed in 0.6 -- Dennis Gascoigne