[VoxBo] vbperminfo

[Daniel Y Kimberg]

Marina Bedny wrote:
> I am trying to use vbperminfo to get a critical threshold with a
> minimum cluster size. Vbperminfo times out before finishing each time
> I run it. That is, I get signed out from the x-terminal before
> vbperinfo finishes.
>
> Any thoughts on how I can get around this?

You could do it in vbbatch, as in:

vbbatch -c "vbperminfo -p /my/data/iterations/permcube /my/data/results.ref 0.05" foo

(The "foo" at the end is just a dummy to tell vbbatch to generate a command line.)

If you're fluent in using vbbatch, you could break it up, as in the
following:

vbbatch -c "vbperminfo -p /my/data/terations/permcube_FILE /my/data/resultsFILE.ref 0.05" 0000 0001 0002 0003 0004 0005 0006 0007 0008 0009 0010

Something like that, depending on how many permutations you have.  All
those 000x tokens get inserted in the command line in place of the
token FILE.  Once you have all the ref files, merge them in a text
editor, and calculate the permutation cutoff you need using vbperminfo
-r (which just takes a second to run).

dan