I'm trying to submit commands to the LSF scheduler with bsub but this command includes a parameter value that must be quoted and contains a semicolon.
Here is a simple command to illustrate my problem
bsub -o t.o -e t.e echo "foo;bar"
it fails with "line 8: bar: command not found", so I thought I could escape the semicolon but this
bsub -o t.o -e t.e echo "foo\;bar"
causes the same error, so does this
bsub -o t.o -e t.e echo 'foo;bar'
I know I can get around it by writing the command to a script file and executing that as the bsub command but in this case I am going to test a number of parameters and it would be so much handier to just modify the bsub command rather than editing a shell script each time.
Thanks for your help!
One simple way I can think of to do this is to use bsub's subshell interface: simply execute bsub <options> from your command line without specifying a command. bsub will then prompt you for a command in a subshell, and you can use quotes in this subshell.
Send the subshell an end-of-file (CTRL+D) to let it know you're done. Here's an example run using something similar to your case but running interactively instead of using -o to capture the output:
% bsub -I
bsub> echo "foo;bar"
bsub> <================[### Hit CTRL+D here ###]
Job <5841> is submitted to default queue <normal>.
<<Waiting for dispatch ...>>
<<Starting on hb05b10>>
foo;bar
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