Ryan Golhar wrote, On 03/29/2011 12:26 PM:
>> Note about multithreaded bowtie:
>> currently the tools use 10 threads (hard-coded in the XML files) - easily 
>> changeable.
> If possible, have the user indicate as a parameter how many threads they wish 
> to use.

This will never happen, at least not in my tools:
The nice user who will kindly use a single thread (or just two or three) has 
not yet been born :)
All users will put the maximum value (or higher) and will choke up the system.

What's more, the underlying submission is using SGE and there's currently no 
way to dynamically change the number of slots a tool is using.
So hard-coded 10 (or other value) it is.

If you do want to allow users to set number of threads, simply change the first 
parameter in the XML file from hard-coded 10 to use a galaxy <param>.


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