This sounds like a good way to solve the problem, I guess I would modify On Thu, Oct 10, 2013 at 6:10 PM, Björn Grüning <bjoern.gruening@pharmazie.uni-freiburg.de> wrote:
Dear all,
some SGE instances will add automatically an semicolon add the end of each command, resulting in a disrupted job, because ';;' are not allowed.
The latest changes to the Bowtie2 wrapper resulting in such a case and a crash in our instance. An easy solution would be to fix the wrapper and omitting the trailing ';' but maybe its better to fix it once for all in the corresponding tools code, patched attached.
I'm not familiar with other Job schedulers so I'm seeking for comments ... it there any disadvantage of removing trailing ';' from the command line?
Ciao, Bjoern
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