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[HTCondor-users] condor_qsub argument "-S" in commandline
- Date: Fri, 06 Feb 2015 09:22:13 +0100
- From: Mathieu BAHIN <bahin@xxxxxxxxxxxxxxx>
- Subject: [HTCondor-users] condor_qsub argument "-S" in commandline
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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