I want to be able to run PHENIX in a shell script, where stdin is accepted as a definition input file. It could be simply specified as the usual POSIX syntax where "-" defines stdin in place of an input file. If the front-end is based too heavily on file suffix mappings, you could add a flag "--stdin=SUFFIX" to define reading stdin as if it had the given SUFFIX. It would also be nice to avoid the duplication of output to both stdout and the .log file. Output can always be sent to /dev/null, but it would be nicer to have either a --quiet flag to suppress stdout, or a DEF option to disable the .log output, or both options to let the user decide. Most other computational programs can be run this way, so I assume that other people would find this useful, especially for running PHENIX from scripts. Hopefully, it is also a fairly easy feature to implement. Thanks, Joe Krahn
The --quiet option exists (phenix.refine --help). Reading from stdin is too tricky as a general feature ("my job hangs") and since phenix.refine cannot work without reading from files (pdb, mtz) and writes many files already, that one extra file doesn't really make a difference. However, you can script phenix.refine from Python, see phenix/phenix/refinement/command_line.py, the run() function, and pass in a list of "external_params", which you could read from stdin. To find out how to pre-process the external_params, see: http://cctbx.sourceforge.net/libtbx_phil.html Ralf
On 09:12 Fri 13 Nov , Ralf W. Grosse-Kunstleve wrote:
The --quiet option exists (phenix.refine --help). Reading from stdin is too tricky as a general feature ("my job hangs") and since phenix.refine cannot work without reading from files (pdb, mtz) and writes many files already, that one extra file doesn't really make a difference.
Don't let that stop you from scripting, though. I often create a file within a shell script for passing into a program, then just clean up afterwards. Same effect. -- Thanks, Donnie Donald S. Berkholz, Postdoctoral research fellow James R. Thompson lab, Physiology & Biomedical Engineering Grazia Isaya lab, Pediatric & Adolescent Medicine Mayo Clinic College of Medicine 200 First Street SW Rochester, MN 55905
participants (3)
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Donnie Berkholz -
Joe Krahn -
Ralf W. Grosse-Kunstleve