Peter Cock wrote:
> 2011/6/2 Nate Coraor <>:
> > Hi Louise-Amélie,
> >
> > I haven't done anything with this code yet, but I wanted to let you know
> > that we'll eventually be adding it, I'm just going to change the
> > implementation slightly.  I'd like to merge the functionality of the csv
> > into an xml config I'm already working on (but haven't yet fully decided
> > on the syntax).  And it should be possible for tools to access these
> > parameters in the command line template.  A lot of our NGS tools have
> > the number of threads to use hardcoded in the tool config, which is bad.
> >
> > --nate
> On a related point, I've previously suggested a $variable could be defined
> for use in tool XML wrappers to set the number of threads. This number
> could come from a general configuration file, or perhaps via the cluster
> settings - the point is the tool doesn't need to know, it just gets told how
> many threads it is allowed.

Yeah, that's the idea.


<?xml version="1.0"?>
        <destination name="default" runner="local"/>
        <destination name="pbs_default" runner="pbs">
            <native_param name="queue">batch</native_param>
        <tool id="upload1" destination="default"/>
        <tool id="bowtie_wrapper" destination="pbs_default">
            <resource type="cores">8</resource>
</job_conf> then knows to translate '<resource type="cores">8</resource>' to
'-l nodes=1:ppn=8'.

Your tool can access that value a bunch, like $__resources__.cores.

The same should be possible for other consumables.


> Peter
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

Reply via email to