Re: [galaxy-dev] tasks (parralelism) and from_work_dir bug

Hi, I have tried to use tasks with tophat2, but I got the following bug.

...

multi.py +153

msg = 'nothing to merge for %s (expected %i files)' \ % (output_file_name, len(task_dirs))

This occurs because tophat2 tool uses from_work_dir feature to get the output files. But on the line: output_files = [ f for f in output_files if os.path.exists(f) ] It returnes an empty list because no real output files exists.

Tophat2 cannot be parallelized because it uses a shared junctions database, and shared objects are not yet supported by Galaxy's parallelism.

That said, it's likely the case that parallelism + from_work_dir do not work together yet; I've created a card for this issue: https://trello.com/c/5fFZSCWn

Best, J.