On Thu, Mar 22, 2012 at 3:34 PM, Daniel Sobral
<dsob...@igc.gulbenkian.pt> wrote:
> Hello,
> For certain tools, like bwa or blast, there is a non-configurable number
> of threads to use inside the tool xml.
> This is inconvenient for certain cluster configurations, where what we
> want is division of a job into multiple jobs (I guess this is what is
> intended by the <parallel> tag), and not creation of threads that may
> wreak havoc in a cluster.
> Is there any reason why bwa and blast have --num-threads=8
> pre-configured in the xml file?

Because there isn't a way (yet) to set this via the universe_wsgi.ini
file. I have asked about this in the past - but can see it is quite
complex and often the idea setting is going to be tool specific.

Note those setttings hardcoded in the <command> tag control
the number of thread in a single job - and I setup my job runners
in universe_wsgi.ini to match (e.g. tell SGE I want 8 threads, or
an entire machine for this job).

Separately to this, in the <parallelism> tag of a tool is a hard coded
splitting strategy (if this experimental feature is enabled in your
universe_wsgi.ini file) for breaking a job into sub-jobs, which are
submitted to the cluster separate. Here again a configuration
mechanism could be nice.

Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:


Reply via email to