Desktop Integration of the Staden Package in KDE on Suse Linux 9

I have installed the Staden package on my laptop. In order to convince other people from my lab to use it, it must be very easy to use. Ideally, they should just need to select some sequences, click and the preprocessing and assembly should be done automatically. In order to achieve that I did the following: I created new mime types for the file manager Konqueror. Konqueror needs this to realize what it should do with a file (or several of them) when you click on them. Go to: Start Menu -> Control center -> KDE Components -> File Associations.

Click "Add", select "All" from the "Groups" pulldown menu and type in "x-staden". In the "Filename Pattern" section add all the file extensions of formats that you want to be handled by staden, e.g. I added *.ab1 (ABI trace files) and *.ebl (EMBL sequence files). In the "Description" field add whatever (Konqueror uses this info for the file type column); I added "Sequence File". Under Application Preference Order, add two applications: First trev (if you quickly want to lock at a trace), second add the script that I assembled and that you can download from here. I put this script into /home/jeltsch/bin, but it can be of course anywhere. You also need to modify the paths to your configurations files, etc. to make it work on your install. You have to modify one thing after you have added the script (including its full path if it is not in your PATH variable) Under the "Application Preference Order -> Execute" tab you will see the following entry (depending where you put the script):

'/home/jeltsch/bin/stadenlaunch'

You have to modify it to look like:

'/home/jeltsch/bin/stadenlaunch' %U

The %U makes Konqueror pass the filenames (including their full path) that were clicked to the script and that is necessary (%u passes only the first filename including full path, %F passes all filenames but without path and %f only the first filename without path).

Actually the modifications that you do within the control center just place a file called stadenlaunch.desktop into your kde configurations directory (~.kde/share/applnk/.hidden/stadenlaunch.desktop): The contents of this file looks like this:

[Desktop Entry] Comment= Comment[en_US]= Exec='/home/jeltsch/bin/stadenlaunch' %U GenericName= GenericName[en_US]= Icon= InitialPreference=2 MimeType=all/x-staden Name=stadenlaunch Name[en_US]=stadenlaunch ServiceTypes= SwallowExec= SwallowTitle= Terminal=false TerminalOptions= Type=Application X-KDE-SubstituteUID=false X-KDE-Username=

As the script generates staden database files (with an .aux ending), I have added another mime type and when I click files edning with .aux, gap4 loads this file.

Actually I just realized I should make a Suse Linux 9 rpm for the Staden package. Then I could decide about the location of the executables and configuration files installation would be easier and end users could just start by clicking their sequence files.