On 10/17/2014 10:39 AM, Peter Cock wrote:
On Thu, Oct 16, 2014 at 11:05 PM, Wolfgang Maier
<wolfgang.ma...@biologie.uni-freiburg.de> wrote:

this is just to make sure: the GALAXY_SLOTS environmental variable set by
Galaxy when running tools will always be a number >= 1 with 1 being the
default if nothing else is configured in the job runner settings ?

Correct ?


Hi Wolfgang,

I believe so, however it is possible it might be unset in a corner case
(please report this as a bug if you see it happen) or a tool could change
the value.

You can use the following bash syntax to set your own default in
the tool's <command> template, e.g.

-num_threads "\${GALAXY_SLOTS:-8}"

Note the colon minus is the special bash syntax, here the default
value is 8 (not minus 8) if $GALAXY_SLOTS is not set. Also note
in the <command> XML you must escape the dollar sign.


Hi Peter,

thanks for confirming. I'm not particularly worried about it being absent.

My use-case is own software that has its own threading config settings, but when run in Galaxy should respect $GALAXY_SLOTS. To do this, it's checking for the presence of the environmental variable and gives it precedence over its own config. What would be problematic though is if in certain situations GALAXY_SLOTS could be "0" or a negative number or something that can't be cast to an int, but Björn's and your answer imply that this won't happen.

By the way, there's one exception from the above precedence rule that I'm planning to implement: if GALAXY_SLOTS defaults to "1", I'll use the config settings instead, essentially giving users the choice if they prefer configuration from Galaxy or from the tool side. Do you think this is a good idea ?


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:

To search Galaxy mailing lists use the unified search at:

Reply via email to