Tophat2 shows error during running

Question

[Whoknows]

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

[Christian]

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

[Ram]

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

[Whoknows]

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

[Ram]

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

[Whoknows]

Yes it was because python 3 in changed to python 2

[Ram]

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

Answer 1

[Devon Ryan]

Try installing python2.

Answer 2

[Rahul Sharma]

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

[Ram]

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