On Fri, Feb 13, 2015 at 11:38 AM, Nicola Soranzo <nsoranzo@tiscali.it> wrote:
Il 13.02.2015 03:17 Peter Cock ha scritto:
Hi Roberto,
It looks like this is a known issue with FASTQ splitting,
https://trello.com/c/qRHLFSzd/1522-issues-with-tasked-jobs-parallelism
I originally broke it during a refactor, but it looks like the discussion died about that that method was meant to do (e.g. FQTOC = FASTQ table of contents?):
https://bitbucket.org/galaxy/galaxy-central/commits/76277761807306ec2be3f1e4...
I'm away from the office so can't try this, but probably all that is needed is to copy and paste the old method get_split_commands_sequential and the old method get_split_commands_with_toc (removed from the base Sequence class in the above commit) into the base Fastq class instead.
Nicola - did you fix this locally after noticing the problem last year?
No, sorry, we disabled Galaxy parallelism because it was using too many cluster nodes.
Nicola
I had similar comments from some of the cluster users after getting it working here - but on balance a well used cluster helps justify future investment in maintaining it. Sorry about not following up on this - I think I might have assumed you would take care of it. Unfortunately I won't be able to test the obvious fix until at least a week later... Peter