On Tue, Nov 27, 2012 at 10:44 AM, Andreas Kuntzagk <andreas.kuntzagk@mdc-berlin.de> wrote:
Hi Alex,
I am not sure if you can call these "surprises".
Well at least it surprised me :-) Didn't want to sound to negative.
Some tools (which I highly appreciate) of Peter have been "parallelised" to get the job done more quickly. I earlier mentioned the ncbi blast+ wrappers but there the tool by itself handles the multithreading. ...
While I can read Python and bash fine it becomes more complicated with perl and R. Don't know if I could easily spot from the code what the number of threads is. So maybe somebody could setup a list of these tools?
regards, Andreas.
The short answer is *every* tool used in Galaxy may be multi-threaded. Sometimes this is done in the binary (e.g. BLAST), others do it in the wrapper when the underlying tool is single threaded (e.g. my SignalP and TMHMM wrappers which Alex mentioned). Sometimes the default is clearly defined in the XML (as a command line switch, e.g. BLAST), sometimes it is defined in a wrapper script, and sometimes it is defined in the tool binary itself (e.g. use all available CPUs). Peter