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.
>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 :(
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