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Tophat2 shows error during running

Hi friends

I installed Tophat2 with all dependencies (bowtie2, Boost, Samtools) but when I want to run tophat, it shows this error:

File "/home/tophat-2.0.14/bin/tophat", line 1003
    except getopt.error, msg:                       ^
SyntaxError: invalid syntax

My python version is 3.4 , how can I fix this problem?

Thanks

rna-seq python tophat
• 7,194 views • link
updated by Ram Ram • written by Whoknows Whoknows

What Devon said. Tophat is not Python 3 clean, so Python 2 is required.

• 1 views • link
written by Christian • Christian

Hi Whoknows, did Devon's suggestion work for you?

• 1 views • link
written by Ram Ram

Yes, tophat has problem with python 2, I had to reinstall linux with python2

• 0 views • link
updated by Ram Ram • written by Whoknows Whoknows

Please accept his answer if that's the case, so this question would be marked as solved by the system.

• 0 views • link
written by Ram Ram

Yes it was because python 3 in changed to python 2

• 0 views • link
written by Whoknows Whoknows

Click the green check mark you see on the left panel of his answer, near the number of votes.

• 0 views • link
written by Ram Ram

2 answers

Try installing python2.

• 0 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

Here is a quick solution without installing/re-installing different versions of python:

# Create a new environment for python 2.7
>conda create -n py2 python=2.7 anaconda
#To activate this environment, use:
> source activate py2

>conda install -c bioconda tophat

>tophat2 --help  ### should work now
#To deactivate this environment, use:
> source deactivate py2
• 0 views • link
updated by Ram Ram • written by Rahul Sharma Rahul Sharma

Use the formatting bar (especially the 101010 code button) to format your post please. I've done it for you this time. Thank you.

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written by Ram Ram

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