[galaxy-dev] Alternative bowtie tools

Assaf Gordon gordon at cshl.edu
Tue Mar 29 13:35:40 EDT 2011


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>.

-gordon




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