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YY-TMU / InPACT

A computational method designed to identify and quantify IPA sites via the examination of contextual sequence patterns and RNA-seq reads alignment.
MIT License
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getopt illegal option --o #7

Open tailana703 opened 2 months ago

tailana703 commented 2 months ago

Hello,

I really would like to use your software on one of the datasets. Can it run on MacOS? I installed it successfully, but when I call InPACT -h the error 'getopt illegal option --o' kept popping up. I tried to remove -o from the 'InPACT' script, but now I get another error: error: argument --annotation_file: expected one argument although I'm sure that I put only one argument after -a in InPACT call.

Any suggestions?

liuxc1995 commented 2 months ago

Hello!

Thank you for raising this issue. The getopt command under MacOS defaults to the FreeBSD version, which is different from the GNU/Linux version. To resolve this, you can install the GNU version of getopt and specify its path in script. Here’s how you can do it:

  1. Install GNU getopt using Homebrew
brew install gnu-getopt
  1. Specify the path of GNU getopt in script
#!/bin/bash 

GETOPT=/xxx/bin/getopt 
ARGS=`$GETOPT XXX`

We hope this helps you resolve the issue. If it doesn't work, we recommend running it on Linux. If you have any further questions, feel free to ask.

Thank you, Liu