How do I download bowtie2 onto my macbook?

Question

I was told I need to first make a virtual environment that runs on Python 3.5. I tried to use the command:

conda create -n p35env python=3.5

But I keep getting the message:

(base) Drews-MacBook-Pro:~ drewramos$ conda create -n p35env python=3.5
Channels:
 - bioconda
 - conda-forge
 - defaults
Platform: osx-arm64
Collecting package metadata (repodata.json): done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - python=3.5*

Current channels:

  - https://conda.anaconda.org/bioconda
  - https://conda.anaconda.org/conda-forge
  - defaults

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

Do I need to add specific channels? If someone can give me a detailed description of how to download bowtie 2, I would be extremely grateful. (I am not very tech savy)

My attempted code:

conda create -n p35env python=3.5
conda activate p35env
conda install bioconda::bowtie2

Answer 1

Generally, my recommendation is to always read and apply the manual first without modifications.

In this case, visit https://anaconda.org/bioconda/bowtie2 which instructs to use the command conda install bioconda::bowtie2. This will take care of all dependencies including the python version. Python 3.5 is very old, it is not surprising this chokes up here.

Indeed creating a separate environment (via conda) makes a lot of sense, since it keeps things tidy and clean. Individual tools might have conflicting dependencies so a fresh environment is almost always helpful. Here, just use conda create --name bowtie2_env, something like that.

Note that using mamba over conda these days is imo recommended as it speeds up things a lot and sometimes solves conflicts better.