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TopHat installation error

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?

tophat
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updated by david.leader • david.leader • written by salamandra salamandra

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

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written by GenoMax GenoMax

it gives the same error

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written by salamandra salamandra

The investigate @Wouter's suggestion below.

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written by GenoMax GenoMax

Looks like a wrong python version issue

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written by WouterDeCoster WouterDeCoster

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

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written by salamandra salamandra

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

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written by WouterDeCoster WouterDeCoster

2 answers

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.

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written by Devon Ryan Devon Ryan

edit the first line in your_tophat_directory/tophat from:

#!/usr/bin/env python

to:

#!/usr/bin/env python2

It worked for me.

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written by Bilal • Bilal

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

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written by alex.v.nesta • alex.v.nesta

This assumes that version 2 of python is installed on your machine and is aliased as python2. In my case a version was present (check with: which -a python) but aliased as python2.7. Hence I had to modify the line to:

 #!/usr/bin/env python2.7

It helps if you understand what you are doing.

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written by david.leader • david.leader

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