On Jul 29, 2011, at 12:44 PM, Assaf Gordon wrote:

> Chris Fields wrote, On 07/29/2011 12:35 PM:
>> On Jul 29, 2011, at 11:00 AM, Assaf Gordon wrote:
>>> Question for galaxy maintainers: have you encountered situations where BWA 
>>> jobs run 'forever' (for days) ?
>>> ...
>>> I'm wondering if this is common enough to justify adding "-A" to the 
>>> wrapper, or is it rare enough and can be ignored.
>> Can it be added as an optional argument?  So that if it is selected, the 
>> setting is passed to the tool, otherwise not.
> Obviously, it can be added to the XML wrapper.
> I'm asking if other people encountered this situation with Paired-end 
> mapping, and whether it's rare or not.

If there are cases where this does occur (as you have pointed out), then the 
XML wrapper should have the option and maybe even a bit of documentation 
pointing this out (even if it is a rare event).  I wouldn't want this running 
on a cluster where users are charged, for instance.

>> From a user's perspective, this kind of parameter makes no sense:
> it basically tells the user: "run BWA without this parameter, and if after 24 
> hours the job is still running, kill it and re-run with this parameter".
> That's not the way to build user-friendly tools :(
> -gordon

It's definitely not intuitive and violates least surprise.  If I explicitly set 
any parameter, I don't expect the application to possibly (and silently) assume 
I am wrong and change it anyway.

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