I can use aln -t n to ask BWA to use multiple cores if I run it in command line, in Galaxy, I did not find this option even i tried "Full Parameter List", anyone know how to do it? (I installed a local Galaxy server with 64 cores, I want to use multiple cores to run my jobs.) Thanks, Frank
On Thursday, November 29, 2012, Fenglou Mao wrote:
I can use aln -t n to ask BWA to use multiple cores if I run it in command line, in Galaxy, I did not find this option even i tried "Full Parameter List", anyone know how to do it? (I installed a local Galaxy server with 64 cores, I want to use multiple cores to run my jobs.)
Thanks, Frank
The number of cores isn't exposed to the end user (although in some cases it might make sense to do so), but is rather down to the Galaxy administrators (in some cases by editing the defaults in the tool XML or wrapper scripts). There was a discussion about this on the list recently. Peter
That will be a pain since so many tools can use multiple cores, and if I edit tool XML file, what will happen is I update Galaxy? Will those edited XML be replaced by the files in Galaxy-dist? Thanks, Frank On Nov 30, 2012, at 3:01 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thursday, November 29, 2012, Fenglou Mao wrote: I can use aln -t n to ask BWA to use multiple cores if I run it in command line, in Galaxy, I did not find this option even i tried "Full Parameter List", anyone know how to do it? (I installed a local Galaxy server with 64 cores, I want to use multiple cores to run my jobs.)
Thanks, Frank
The number of cores isn't exposed to the end user (although in some cases it might make sense to do so), but is rather down to the Galaxy administrators (in some cases by editing the defaults in the tool XML or wrapper scripts). There was a discussion about this on the list recently.
Peter
On Fri, Nov 30, 2012 at 2:54 PM, Fenglou Mao <fenglou@gmail.com> wrote:
That will be a pain since so many tools can use multiple cores, and if I edit tool XML file, what will happen is I update Galaxy? Will those edited XML be replaced by the files in Galaxy-dist?
If you modify a tool bundled with Galaxy, then when you do an hg update in simple cases it would all be handled automatically. However, if there was a change in the same part of the code, you would have to do a manual merge (the simplest route is just take the 'official' changes from the Galaxy team, and in the short term discard your local change). i.e. Not a good idea for long term maintenance. The other thread I was referring to was discussing how to move the thread settings into the Galaxy configuration files instead. Peter
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Peter Cock