Tophat not installing with Biostar Handbook

Question

[k.e.pendleton]

I'm working from the Biostar Handbook and trying to do the alignment with tophat. I'm on page 480 for reference.

I was able to successfully run

$ bowtie2-build $REF $IDX

However, then it says that I need to change the invocation of the aligner to

$ tophat -G $GTF -o tophat_hbr1 $IDX $R1 $R2
bash: /usr/bin/tophat: No such file or directory
(bioinfo)

And that's my output. If I do which tophat, nothing comes up, so it seems like it's just not there. So, I tried to install tophat with

$ conda install tophat
Fetching package metadata .................
Solving package specifications: .

UnsatisfiableError: The following specifications were found to be in conflict:
  - python 3.6*
  - tophat -> python 2.7*
Use "conda info <package>" to see the dependencies for each package.

(bioinfo)

I saw some solutions online for changing a line of code in tophat to do this, but I don't even know where that file is. I can downgrade python, but I'm not sure if that will work, and I'm worried that I'll break other things if I do. Also, when I do

$ ls /usr/bin | grep python
dh_python2
dh_python3
python
python-config
python2
python2-config
python2.7
python2.7-config
python3
python3.4
python3.4m
python3m
x86_64-linux-gnu-python-config
x86_64-linux-gnu-python2.7-config
(bioinfo) 
moltres@moltres-ao ~/biostar/Sequencing/griffith
$ python -V
Python 3.6.3
(bioinfo)

I see a bunch of different python versions, and I'm not sure if I should switch between them or what.

I'm a little frustrated because I bought this book because I'm a beginner, but I keep running into errors that are over my head. I'd really appreciate help here.

[Chirag Nepal]

Authors of Tophat paper recommend not to use the software anymore.

Please stop using Tophat https://t.co/Es4ohxOEyx Cole and I developed the method in *2008*. It was greatly improved in TopHat2 then HISAT & HISAT2. There is no reason to use it anymore. I have been saying this for years yet it has more citations this year than last #methodsmatter

— Lior Pachter (@lpachter) December 2, 2017

[k.e.pendleton]

That's cool. If I were doing real analysis, that would matter. I'm just trying to learn basics and follow the book. Thanks for the input, though.

[GenoMax]

As you can see above TopHat requires python v.2.x (and won't run properly with python v.2.x). Your default python is the latest v.3.6.

I am going to suggest that you try the solution given in this thread for now: A: Tophat2 shows error during running (> in the thread is the system prompt so that should be $ for you).

Tagging Istvan Albert to make him aware of this hurdle for new users.

Answer 1

[h.mon]

Create a new environment for Tophat:

conda create -n tophat2 tophat2

should create a new environment and install Tophat2 and its correct dependencies.

[cpad0112]

i guess you can add python version as well in conda environment (for eg. python=2.7 )

[k.e.pendleton]

This is correct. Also, I didn't realize that there's a GitHub page especially for the book, so I'll try to target that instead if I think it's a book specific issue. I had also posted the question there since I thought it might be more appropriate, and I essentially got the same response.

https://github.com/biostars/biostar-handbook-issues/issues/37

Thank you for your help!