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' (line ~340) and replace: try: shutil.copy(file_name, self.get_filename(obj, **kwargs)) except IOError, ex: log.critical('Error copying %s to %s: %s' % (file_name, self._get_filename(obj, **kwargs), ex)) by: try: if os.path.isdir(file_name): dir_name = self._get_filename(obj, **kwargs) os.remove(dir_name) shutil.copytree(file_name, dir_name) else: shutil.copy(file_name, self.get_filename(obj, **kwargs)) except IOError, ex: log.critical('Error copying %s to %s: %s' % (file_name, self._get_filename(obj, **kwargs), ex)) - Nik. On Thu, Mar 28, 2013 at 7:06 PM, Nikhil Joshi <najoshi@ucdavis.edu> wrote:
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 images directory is a zero-length *file*. I seem to recall having this problem before and finding a solution to it, but now I can't seem to find it. Any ideas?
- Nik.
-- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)
-- Nikhil Joshi Bioinformatics Analyst/Programmer UC Davis Bioinformatics Core http://bioinformatics.ucdavis.edu/ najoshi -at- ucdavis -dot- edu 530.752.2698 (w)