TopHat installation error

Question

[salamandra]

I'm new to ubuntu and i am trying to install tophat-2.1.1.Linux_x86_64 in an ubuntu 16.04 LTS system.

I unpacked the binary version to the home directory, and because ~/bin is in my $PATH I did:

cd 
tar xvfz tophat-2.1.1.Linux_x86_64.tar.gz
cd ~/bin
ln -s ~/tophat-2.1.1.Linux_x86_64/tophat2

And I got the following error when type tophat2:

File "/home/tania/tophat-2.1.1.Linux_x86_64/tophat", line 1003
    except getopt.error, msg:
                       ^
SyntaxError: invalid syntax

What am I doing wrong?

[GenoMax]

Try tophat2 -h. (or -help) It is expecting you to provide some input.

[salamandra]

it gives the same error

[GenoMax]

The investigate @Wouter's suggestion below.

[WouterDeCoster]

Looks like a wrong python version issue

[salamandra]

to use tophat Python version 2.6 or higher is required, and mine is Python 3.5.2, so it isn't cause of that

[WouterDeCoster]

See http://seqanswers.com/forums/showthread.php?t=17514

[WouterDeCoster]

Oh and stop using tophat for new projects, it's deprecated

Answer 1

[Devon Ryan]

You're using python3, which won't work for tophat2 (or bowtie2). Anyway, there's no reason to ever use tophat2 for new analyses. Use STAR or BBmap.

[WouterDeCoster]

.toggled status to accepted.

Answer 2

[Bilal]

edit the first line in your_tophat_directory/tophat from:

#!/usr/bin/env python

to:

#!/usr/bin/env python2

It worked for me.

[alex.v.nesta]

Thanks, this worked for me. I know tophat hasn't been updated since 2016, but some pipelines still use it.

[javanokendo]

This works for me...thanks