On Jan 23, 2012, at 6:07 PM, Jaime Frey wrote:
> Hello, everyone.
> I'm working on a Condor job-runner module for Galaxy that can provide better
> integration than the existing drmaa module. I'm sure I'll have many questions
> as I work on this module, but I have just a few to start with:
> * What versions of Python does Galaxy support (i.e. which newer features of
> Python do I need to avoid)?
The current minimum is 2.5, and there are no plans to drop it any time soon
(2.4 was dropped only a few months ago).
> * What is the status of the 'staged' cluster deployment? The wiki says it's
> not in active use or development. But our Condor cluster doesn't have a
> shared filesystem, so we need to stage data files to/from the execute nodes.
You can see the code over in lib/galaxy/jobs/runners/pbs.py. I haven't used it
in a couple of years, and there would definitely some potential problems as
> * The wiki also says that even with the staged cluster deployment, a shared
> directory (galaxy_dist/database/tmp by default) is required for some tools.
> These tools write temporary files on the Galaxy server and read them on the
> execute node. Does anyone know which tools those are? Are these files ever
> written after the job is handed to the batch system? Do these tools write
> files into galaxy_dist/database/tmp on the execute ndoes and read the files
> on the Galaxy server?
Unfortunately I don't have a list, but see the tools which use work_dir (such
as tophat) and any that pass the extra_files_path attribute.
> Thanks and regards,
> Jaime Frey
> UW-Madison Condor Team
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