[phenixbb] phenix.phaser params.eff output directory

G Y gysubscribe at gmail.com
Tue Jul 26 02:32:22 PDT 2011

Hi Nat,

Thanks for your reply.

I am now writing a bash script to call phenix.phaser. I do not want to use
shell command like mv or cp the files to desired directory, as I will
generate a lot outputs. I hope I could change some parameters in params.eff
to achieve this goal more easily. But as you said, it is not possible,
right?  Just for confirm. Thanks for your reply.


On Mon, Jul 25, 2011 at 7:41 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Mon, Jul 25, 2011 at 8:09 AM, G Y <gysubscribe at gmail.com> wrote:
> > I am writing a script for phenix.phaser. The keyword "output_dir" seems
> not
> > work. In params.eff file I give it a line like:
> > solution = None
> > output_dir = /home/.../somedir/
> > ...
> > But I can not generate output file in the specified directory(somedir in
> the
> > above case). The output files are always put in current working
> directory.
> > Did I choose a wrong keyword to do this? What would be the correct way?
> This parameter exists solely for use in the GUI; it won't have any
> effect on the command line.  In hindsight this probably wasn't the
> best way to handle it - I should have enclosed it in a "gui {}" block
> to make the purpose clear.  However, the intention was always that the
> program will output files to the current working directory, as this
> simplifies things considerably for the GUI.  Depending on what you're
> trying to accomplish, calling phenix.phaser from a shell or Python
> script which changes to (and creates if necessary) the desired
> directory is probably the best solution.
> -Nat
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