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cole-trapnell-lab / cufflinks

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cuffmerge invalid syntax #103

Open Juliajuli opened 6 years ago

Juliajuli commented 6 years ago

hello, I am trying to use cuffmerge tool but it is showing error reports in python script. can you please suggest me what to do with that. 

molbiolab@molbiolab:~/Documents/Juli/Practice/cufflinks-2.2.1.Linux_x86_64$ ./cuffmerge
  File "./cuffmerge", line 95
    except getopt.error, msg:
                       ^
SyntaxError: invalid syntax
apollobovey commented 4 years ago

same error reports when i want to see --help or -h info.

Winnie912 commented 4 years ago

I meet this problem as well. And it doesn't work when I redownload cufflinks. I read on the Internet that a lot of people are having this problem.But it's still unresolved. Hope it can be settled as soon as possible!

arh223 commented 4 years ago

I was able to get around this error by specifying an earlier version of python

python2.7 /usr/bin/cuffmerge [add what processes you want to run]

TCAG-LifeSciences commented 2 years ago

HAS THIS BEEN RESOLVED YET

gunjangunjan22 commented 1 year ago

I have encountered the same issue while using cuffmerge, I used py2 (python 2) environment in a miniconda, which worked well for me. If you have Miniconda on your system, here is a code

conda create --name py2 python=2.7 activate py2 and then run ./cuffmerge (options)

Thanks Hope this works!!