Installing Staden 2003b on Suse 9

1. Download the sources.
2. cd into /usr/local and become su.
3. tar -xvzf /home/jeltsch/Documents/staden_linux_2003.0b1.tar.gz (jeltsch is my usename, thus has to be replaced for other users!!!!)
4. Edit your .bashrc file by adding the following two lines to its end:
export STADENROOT=/usr/local/staden_linux_2003.0b1
. $STADENROOT/staden.profile
5. Ready.
6. I usually get sequencing data in the form of abi files. Those files I put into a new directory together with other sequence data files (plain text). Then I run a script, that shortens the filenames to make them compatible with the Staden package, preprocesses the data using pregap4 and invokes the gap4 program:

for i in `ls *_Run_ABI_3100_*.ab1`; do
echo "Renaming $i"
mv $i `echo $i | sed "s/_Run_ABI_3100//"`
rm -f *Run_ABI_3100_*
rm *.txt
ls *.ab1 *.seq > tracefile.list
/usr/local/staden_linux_2003.0b1/linux-bin/pregap4 -nowin -config /home/jeltsch/sequences/pregap4 .defaultconf -fofn tracefile.list