On Thu, Oct 17, 2013 at 5:04 PM, John Chilton <chil...@msi.umn.edu> wrote:
> On Thu, Oct 17, 2013 at 5:49 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> On Thu, Oct 17, 2013 at 11:36 AM, John Chilton <chil...@msi.umn.edu> wrote:
>>
>> (And with the job splitting not being enabled by default, I am
>> aware that I am in a relatively small group of Galaxy admins
>> using it.)
>>
>> I don't think my fix hurts non-task split jobs, but I will now try your
>> fix on the default branch:
>
> I think it will in at least some cases if metadata is getting set
> externally, I don't see how it is preventing some commands from
> running together, I could totally be wrong though.
>
> At any rate, I tested the version with my fix on your blast wrappers,
> with task splitting on and off, submitting to a DRM and using the
> local job runner, and they all seemed to work. Let me know if your
> galaxy instance is unconvinced.

Seem fine so far :)

>> This appears to also address a metadata issue, which if I am lucky
>> may be the fix for this issue?:
>>
>> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-October/017031.html
>
> I doubt your luck is so good. That problems looks like some sort of
> disk caching issue to me (galaxy process and worker node having
> inconsistent views of the same file system), I doubt this will fix it.
> Though hopefully I am wrong on both counts :).

Disk caching makes sense as a root cause - I've not had this
happen consistently or reproducibly yet so it may well return.

> Thanks for reporting the problem and the fix!
>
> -John

No problem, thank you for addressing it so promptly.

Peter
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