Peach Compatibility Guide

Software in general

Peach can be used to run any program or script as long as the participating computers have access to the relavant binaries.  These programs or scripts to be run must not require interactive input from the user.

Bsoft

Bsoft is completely compatible with Peach.  The Bsoft package was used extensively during all phases of the development of Peach.  In order to use Bsoft programs with Peach, the Bsoft environmental variables must be updated into the .Peachpath file located in the Peach program directory.

Execution of Bsoft programs is accomplished by typing psubmit infront of the Bsoft command line.  For example, to bin an image using the program bint, type the following:
psubmit bint -bin 3 input.tif output.tif

Suggested compatibilites with other electron microscopy imaging software

These suggested steps have not been tested on the following popular packages which are listed in alphabetical order.

EMAN

EMAN allows the user to run the various lower level command line programs.  In order to use EMAN with Peach use the following steps:
  1. Simply write a script file (for example "eman.pl") that executes EMAN commands with the appropriate parameters and inputs.
  2. Submit it to Peach by typing psubmit "eman.pl"

Imagic

Imagic has a batch accumulation mode that allows the user to build up a c-shell script.  In order to use Imagic with Peach use the following steps:
  1. Use this accumulation feature to create a c-shell script (for example "imagic")
  2. Submit it to Peach by typing - psubmit "imagic.b"

Spider

Spider has the ability to be run in batch mode.  In order to use Spider with Peach use the following steps:
  1. Write a spider batch file called bat01.spf for example
  2. Submit it to Peach by typing - psubmit "spider spf/ext @bat01"
(spf is a batch file extension, ext is a data file extension and bat01 is name of the batch file without its extension).

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Updated 2005-02-16, Peter Leong