line 5 of run_xander_skel.sh

[karoraw1]

causes it to fail unconditionally

[gunturus]

can we get a little more information. Is there an error in particular?

[karoraw1]

I tried to follow the README example i.e.

bash
cd testdata
cp ../bin/xander_setenv.sh my_xander_setenv.sh
# edit the parameters in my_xander_setenv.sh 
../bin/run_xander_skel.sh my_xander_setenv.sh "build find search" "nifH nirK rplB nosZ"

In the last step, run_xander_skel.sh fails when it gets to line 26. It attempts to run run_xander_build.sh from BASEDIR=/mnt/research/rdp/public/RDPTools/Xander_assembler/bin instead of from a directory on the local filesystem.