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FelixKrueger / TrimGalore

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
GNU General Public License v3.0
461 stars 150 forks source link

TrimGalore only detects python 2, but I have python 3 #78

Closed ejwright39 closed 4 years ago

ejwright39 commented 4 years ago

I suppose this isn't an issue with TrimGalore per se, but I'm running Ubuntu 18.04 (Linux kernel 5.0) and I have python 2.7 on my system specifically for conda and conda envs for programs that require python 2. I also have python 3.6 for everything that requires python 3. By default when I enter "python --version" I get "Python 2.7". As such when I start trim_galore it says multicore support disabled. I assume this is because it does the same "python --version" check. How do I change my default python version in my PATH? I've read that this can cause serious issues though? Or perhaps how do I tell TrimGalore to look for "python3 --version" rather than just "python --version"?

FelixKrueger commented 4 years ago

This Python 2 vs 3 discrepancy is just one of a kind, I will be happy to see the back of it some day...

Couldn't you try to open Trim Galore in a text editor, look for python commands and mannually change them to python3? Let me see how it goes.

ejwright39 commented 4 years ago

Yes it really is a pain. I actually just did that. It still says multicore support not enabled. Is cutadapt also checking python --version? Not sure if trim_galore is requesting anything from cutadapt?

FelixKrueger commented 4 years ago

That might well be... Could you also edit the first line of Cutadapt itself to point to #!/usr/bin/env python3 ? I am fairly new to the Python field, so maybe some googling might help if this fails?

ejwright39 commented 4 years ago

Tried that too. Still says Multicore support not enabled. Not a huge deal. The various versions and installations of python are a mess on my system. It's probably some crazy eccentricity of my personal setup more than an issue with TrimGalore.

EDIT: I went ahead and specified cores anyway using -j 4 and it worked fine. The 'multicore not enabled' warning must just be some result of my tangled mess of Python versions. But in actual use it seems fine. It calls up Python3.6 and I'm seeing multiple cores loaded.

Thank you for the prompt attention to my issue that turned out to not be an issue

FelixKrueger commented 4 years ago

Excellent, I am glad you got it to work on your slightly eccentric system eventually!