Il giorno gio, 13/06/2013 alle 18.06 +0100, Peter Cock ha scritto: > On Thu, Jun 13, 2013 at 6:02 PM, Nicola Soranzo <sora...@crs4.it> wrote: > >> > >> There are two issues here, one that we would like to be able to > >> handle multi-threading better via Galaxy configuration on a > >> per-tool level, but for now it must often be hard coded or > >> done via tool-specific environment variables. > > > > Regarding the configuration of multi-threading for BLAST+ tools, instead > > of hardcoding "-num_threads 8" in the XML files, I'd like to do > > implement something like this: > > > > http://toolshed.g2.bx.psu.edu/repos/jjohnson/cdhit/rev/cca0838c1597 > > > > What do you think? Should I prepare a pull request to discuss at > > GCC2013? > > That's a sensible idea, something like $BLASTTHREADS as > an environment variable?
I was thinking something like BLAST_SITE_OPTIONS='-num_threads 8', which could also include other parameters (e.g. memory limits) in the future. > I'd still prefer something built into Galaxy like $THREADS or > $GALAXYTHREADS or whatever which can be sets with a > default value and adjusted in the per-tool job runner setup > (e.g. send BLAST jobs to this cluster queue with 16 threads). > > This is definitely a good general topic for the tool authors > and/or BLAST wrapping BoF sessions at the conference: > http://wiki.galaxyproject.org/Events/GCC2013/BoF/ToolDevelopers > http://wiki.galaxyproject.org/Events/GCC2013/BoF/GalaxyBlast > > Peter ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/