Change python version to run cutadapt

0

Entering edit mode

6.1 years ago

dllopezr ▴ 130

Hi everyone!

I want to run cutadapt with a lot of shotgun sequences, but it takes to much time to run. Reading the documentation of this tool I found that multithreading is support but only when Python 3.3 or later is used. By default, my python version is 2.7 but I also have installed python 3.4. I'm working as a user in a server and until now I don't have permissions to change the default version.

There is an option to run the program with other versions of python rather than default?

Thank you so much

cutadapt python version • 2.5k views

ADD COMMENT • link 6.1 years ago by dllopezr ▴ 130

2

Entering edit mode

Hello,

which operating are you using? If you are under linux you could try setting an alias for python in you .bashrc

$ echo 'alias python="/usr/bin/python3.4"' >> ~/.bashrc

(Restart the terminal afterwards)

Another way is to use bioconda (You can take a look at the first part of a tutorial I've wrote on how to use it)

fin swimmer

ADD REPLY • link 6.1 years ago by finswimmer 16k

0

Entering edit mode

Any follow up, dllopezr?

ADD REPLY • link 6.1 years ago by Kevin Blighe 88k

1

Entering edit mode

Hi Kevin! I Tried the @finswimmer solution but a "permission" message appear. Tomorrow I will talk to my system administrator and I will try again.

I will keep you notified. Regards!

ADD REPLY • link 6.1 years ago by dllopezr ▴ 130

Login before adding your answer.