NEXUS Tool Testing Introduction
===============================

The python scripts in this directory that are intended to be run are:

* accept_nexus.py


Properties file
===============

The scripts expect that you have a properties file that explain where the 
NEXUS-using tools are found.
The properties file can be a file called "tools.properties" or ".nexus_tool_check_rc"
in this directory, or can be a file named ".nexus_tool_check_rc" in your home directory.

The format of the file is that of Java properties file.  In this case it is:

tool-version-number=path

where:

* `tool` is the name of the tool
* `-version-number` is an optional suffix specifying a tag to the version
* `path` is the path to the location on your machine needed to test the file.


Supported tools, with their accepted arguments:
===============================================

+--------------------+---------------------------------------------------------+
| cipres_nexus_check | path cipres_nexus_check.py (note your env must already  |
|                    | be configured to allow you to run cipres_nexus_check.py)|
+--------------------+---------------------------------------------------------+
| paup               | path to paup executable                                 |
+--------------------+---------------------------------------------------------+
| mb                 | path to MrBayes executable                              |
+--------------------+---------------------------------------------------------+
| bio_nexus          | path to directory where Bio::NEXUS was installed (parent|
|                    | of Bio/NEXUS.pm this path will be added to the PERL5LIB |
|                    | during testing.                                         |
+--------------------+---------------------------------------------------------+


Example properties file
=======================

cipres_nexus_check=/Users/mholder/cipres/bin/cipres_nexus_check.py

paup-4.0b10=/Users/mholder/shell/cipres_tools/bin/paup

mb-3.1.2="/Users/mholder/shell/cipres_tools/bin/mb"

bio_nexus-0.67=/Users/mholder/installed/lib/perl5/site_perl