Re: [galaxy-dev] directory copies as zero-length file from job_working_directory?

2013-04-20 Thread Nikhil Joshi
So I found the solution we used before... is there a reason this code hasn't been changed? Is there a better way to do what I want to do? Here is the solution we used: Yes, you have to modify lib/galaxy/objectstore/__init__.py: In class DiskObjectStore find the function 'update_from_file'

Re: [galaxy-dev] directory copies as zero-length file from job_working_directory?

2013-04-20 Thread Rob Leclerc
Hi Nikhil, I've encountered this issue as well when using the API. Some scripts were using a 5 second sleep default to allow for copying the file to the output directory, but I found that I needed up to 15 seconds (occasionally that's not even enough). Cheers, Rob Rob Leclerc, PhD P: (US)

Re: [galaxy-dev] Any hint on how to use Galaxy within virtualenv?

2013-04-20 Thread Jean-Francois Payotte
Hi Dannon, We are using Galaxy distribution from February 8, 2013. We didn't have time to update to the April 1st distribution yet. I think the update is planned for next Monday. Is this issue supposed to be solved in the February 8 distribution as well? Or only in the latest (from April 1st)?