In addition to these two folders and three SeqPup files, the program will automatically create a personal preferences file in you computer when you first run it. These preferences come from the SeqPup.prefs file. The preferences file created on your system will be something like this
System Folder:Preferences:seqpup.cnf - MacOS
c:\windows\seqpup.ini - MS Windows
~/.seqpuprc - Unix
The program will save various configuration information to this file. You may edit this with a text editor. You may delete it and a new one will be generated from the SeqPup.prefs file. You may not edit it while the program is active (any such changes are lost). When the program is updated in the future, new preferences are added, using the label
[version=123]
to indicate the version number.
The preference file format is as follows:
- Logical sections are indicated in brackets [section].
- Variables are denoted with a "name=value" format.
- Line starting with ";" indicates a comment and will be ignored.
The current release of the program may require some fiddling to install correctly. This
is a known problem, and will be corrected in future releases. You will want to look at and probably edit the file "SeqPup.prefs".
The following sections are important in getting the program to work right, and may need to be edited.
[paths]
temp=
tables=tables
apps=apps
[data]
codon=tables:codon.table
renzyme=tables:renzyme.table
color=tables:color.table
If you use this on a Unix system or an MS DOS system, the current configuration should work if you start the program from its folder, e.g.,
cd /path/to/seqpup/
./SeqPup
A perhaps better way for Unix or MSDos systems is to set the environemntal variable called "SEQPUPHOME" to the path to SeqPup's folder, then you can run the program from any local directory (v.0.5 or 0.4k)
setenv SEQPUPHOME /path/to/seqpup/
SeqPup
But as is common on Unix, if you want to install this for use from any directory, you will currently need to edit the prefs file and put a fixed path to the SeqPup folders in it, as
[paths]
temp=/tmp
tables=/long/path/to/seqpup/tables
apps=/long/path/to/seqpup/apps
If you run SeqPup first, then decide to change parts of the prefs file, you can have all users prefs be updated if you add the new prefs after a new version number. This is the procedure:
a) add a higher version number at the end of the SeqPup.prefs file
[version=6]
b) add changed preference sections and values after that. You need not remove or edit the original values (I hope...).
So for instance if the highest verson value in the prefs file is 5, then add this at the end of the SeqPup prefs to get all users preferences updated:
[version=6]
[paths]
tables=/new/path/to/seqpup/tables
apps=/new/path/to/seqpup/apps
An important caveat with this: New distributions of SeqPup will use new version values to trigger preference updates. If the new distribution has a lower version value than you have used, it won't trigger an update.
Child applications are configured for use with the SeqPup.prefs file. Please see below the section Child Tasks.