Staden Package

Several software installations modify the PATH environment variable. There are many different file that are read during bootup that contribute to the final PATH variable. Several software installs, however, break exisiting PATH entries. Among them is the Staden package. The staden installation instruction advise to include the following lines in ~/.bashrc:

export STADENROOT=/usr/local/staden-linux-rel-1-4 . $STADENROOT/staden.profile

In order to quickfix PATH problems, you can give the full path that you need in /etc/profile.local:

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.

Because I don't have Netscape installed on my computer, the help function of Staden doesn't work automatically. During the staden course James told be to look into /usr/local/staden-linux-rel-1-4/lib/tk_utils/help_netscape.tcl I might do so, but as a quick fix I made a symbolic link to mozilla: sudo ln -s /usr/bin/mozilla /usr/bin/netscape And this really works. I also tried it succesfully with Konqueror: sudo ln -sf /opt/kde3/bin/konqueror /usr/bin/netscape