Toqa, In answer to your first question - you can use the "bash" interpreter as follows:
<command interpreter="bash"> shell_script.sh arg1 arg2 ... argN </command>
I'll leave your second question to someone more qualified than me. Cheers, Graham
Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601
On 21/11/2011 16:09, "Toqa Manasrah" tmanasrah1@student.gsu.edu wrote:
Hi everybody,
I am integrating my software ViSpA inside galaxy and I have two questions: 1: the main program is a shell script (.sh) which call another shell script, which call Java executables. should I include any interpreter inside the .xml <command > tag? and what that should be?
- how to guarantee that the output files destination are on the use
local host rather than the server which is running galaxy?
Thanks and regards,
Tuqa.