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Alternatively, if you would like to change the output directory, copy the file, make the modifications and source your own file:
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cp /home/mktrost/seqshop/setup.txt ~/setup.txt
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nedit ~/setup.txt
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source ~/setup.txt
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(You can use your favorite editor instead of nedit. I typically use emacs, but nedit is more like Windows.)
      
== Examining GotCloud Align Input Files ==
 
== Examining GotCloud Align Input Files ==

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