
rovf
Veteran
Jul 27, 2012, 4:12 AM
Post #3 of 7
(2722 views)
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Re: [sooper] help with shell script
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You really should post this in a forum for Shell scripts, but.... I would pass the working directory as parameter to the shell script (instead of asking the user for input), because this will make your script useful in a wider context. You didn't point out, which Shell you are going to use, but from the way you write your pathes, I assume that you are on a Unix like system. Here is an example for zsh (it would work likewise with bash and, AFIK, with ksh, ash and Bourne Shell):
#!/bin/zsh -f # Ensure that the user supplied a directory : ${1?Parameter missing - must be user directory} perl run_pipeline.pl -fork1 -UQseqToTagCountPlugin –w mypath/$1 -e ApeKI -endPlugin -runfork1 .... Of course you would have to adapt the #! line according to your system.
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