Installing SeqPup
 
SeqPup is distributed over the Internet in archive files.  The archive 
format used is commonly available on the computer system you use (HQX 
self-extracting for Macintosh, ZIP for MS Windows, and tar + Gnu ZIP for 
Unix).  There is one primary program, several document and data files, 
examples, and child application programs. 

The current organization of files used by the program is:
  SeqPup        -- execuable, called "seqpup.exe" in MSDOS
  SeqPup.help   -- this document, in Microsoft RTF format
  SeqPup.prefs  -- settings for the program, in text format.

  tables/ -- data files, required for Restriction maps, 
            translate and some other functions.  These are 
            standard bioinformatics data files available and 
            updateable from various sources.
    codon.table   -- table of codon preferences, in GCG format
    renzyme.table -- REBase data file, for restriction maps, in GCG 
                     format
    color.table   -- table of color values for display of bases
    hum.cod, tob.cod, eco.cod, and other codon preference tables that 
       can substitute for codon.table at your preference

  apps/ -- a selection of external analysis applications. 
    clustalw  -- multiple sequence alignment
    cap2  -- contig alignment
    fastDNAml -- phylogenetic analysis of sequences
    lsadt     -- De Soete least squares phylogeny analysis
    drawtree  -- draw unrooted tree, from Phylip
    drawgram  -- draw cladogram, from Phylip


Note for Sun systems:  This program requires the Motif run-time libraries 
that are commonly found on other XWindow systems.  Motif is not standard 
on SunOS and is not part of Solaris until verson 2.4.  If you have 
Solaris 2.3 or earlier, or SunOS, and do not know that your system 
includes Motif, then you will need the version with statically bound 
Motif libraries (SeqPup-sunos-mostat.gz).  

If you have Solaris 2.4, or a version where Motif libraries are present, 
you may still need to configure the system to let SeqPup know where they 
are.  In a Solaris 2.4 system, where motif lives in /usr/dt/lib by 
default, this may be needed to run successfully:
setenv LD_LIBRARY_PATH "$LD_LIBRARY_PATH":/usr/dt/lib




Installing preferences
 
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

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 wonÕt trigger an 
update.

Child applications are configured for use with the SeqPup.prefs file.  
Please see below the section  Child Tasks.

.
