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?
2. 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.
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.
On Nov 21, 2011, at 11:09 AM, Toqa Manasrah 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?
Hi Tuqa,
Can you clarify this second question? I'm not sure what you're asking.
Thanks, --nate
Thanks and regards,
Tuqa. ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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-
graham etherington (TSL) -
Nate Coraor -
Toqa Manasrah