installing Trimmomatic on MacBook

Question

[gina02]

I am using a M1 MacBook Pro and i'm not able to install trimmomatic successfullly. I tries using conda installer and ended up with an error. how to install trimmomatic from scratch?

[Michael]

It should work fine, I don't have a M1 Mac to test but there shouldn't be anything in the way in principle. You need to provide a little more detail for us to figure it out, including the exact commands you tried and exact error messages. My first guess is that you might be lacking Xcode tools or have the wrong (possibly from simply transferring software from your old mac) version of conda. There ought to be a native conda installer, see here https://stackoverflow.com/questions/65534042/anaconda-and-upgrading-to-new-m1-mac

Upon checking the Miniconda documentation website, conda doesn't seem to have support for M1 macs yet, so you might have to try the link given above.

Answer 1

[GenoMax]

I tries using conda installer and ended up with an error.

What was the exact error? trimmomatic works fine on a M1 Macbook.

Follow the minimal directions to install conda and set the proper order of channels (this is important): https://bioconda.github.io/user/install.html

Once you do that:

# to install trimmomatic in a new env
conda create -n trimmomatic trimmomatic
#activate that env to use trimmomatic
conda activate trimmomatic 

[gina02]

Ive installed Conda as per the instructions , and this is the code I used to set up the channels

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

this is the error I'm getting zsh:

 command not found: conda
zsh: command not found: conda
zsh: command not found: conda

[GenoMax]

It appears that you did not allow conda to initialize itself when you installed it. Try this

source ~/miniconda3/bin/activate 
~/miniconda3/bin/conda init zsh

Then close the shell and open a new one.

[gina02]

it works perfectly now thanks a lot