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 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.