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) +1

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' (lin

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

2013-03-28 Thread Nikhil Joshi
Hi all, So I have a tool that I am writing a wrapper script for that produces a directory of images as one of its outputs. This directory gets created just fine in the job_working_directory, but then when the job finishes and the contents of the job_working_directory are copied, the copy of the i