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The general command to run the software is eitherone of these:
| Code Block |
|---|
java -jar readseq.jar java -cp readseq.jar run |
This should return the help for readseqReadseq.
(Why the funny invocation? You are actually using the command java and telling it where to find a "jar" file of java code to run. The -jar and -cp options run it in different ways. It's pretty confusing.)
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It's a bit hard to figure out because, unlike most conventions, it takes the unnamed arguments before the optional flag arguments and , there is no example command, and you have to switch -jar to -cp. Search online for usage examples when you can't figure something out from the help.
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