On Fri, Feb 13, 2015 at 11:38 AM, Nicola Soranzo <nsora...@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/76277761807306ec2be3f1e4059dd7cde6fd2dc6#comment-820648
>>
>> 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
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