[HTCondor-users] condor_qsub argument "-S" in commandline

[Mathieu BAHIN <bahin@xxxxxxxxxxxxxxx>]

Hi all,

I would like to execute this commandline with condor_qsub:
samtools view -Sb <file.sam>

So I tried:
condor_qsub -S /bin/bash -b y samtools view -Sb <file.sam>

It doesn't work and I guess it is beacuse the "-S" argument of the 
commandline is in conflict with the condor_qsub "-S" argument.
I tried to encapsulate the commandline within quotes but it didn't 
change anything.

Is there a way to do that ? (Except creating a command file to run)

Cheers,

--
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| Mathieu Bahin
| IE CNRS
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| Institut de Biologie de l'Ecole Normale SupÃrieure (IBENS)
| Biocomp team
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