If you’re going to do things with the bash command line, you’ll inevitably have to install a number of packages / dependencies. Having a package manager can help with this, along with virtual environments, that allow you to keep the versions of packages you need for different purposes relatively organized. For package managers, I have tended to like Anaconda the most. So install that. I’m not going to go through the steps here, since I already have it installed, so I’d really have to go out of my way to try to describe that. But it should be pretty straightforward.
Well, I want to create and run a script using biopython, but I don’t already have it installed on this computer, so this seems like a nice time to make a virtual environment for it. The steps I did were as follows:
- Create a virtual environment for biopython.
$ conda create -n biopython
- Activate the virtual environment
$ conda activate biopython
- Next, install biopython.
$ conda install -c conda-forge biopython
That should be it. Whenever you want to deactivate the virtual environment, you can type:
$ conda deactivate
5/17/22 edit: I’ve been doing some image analysis in python, that requires installing some of the following packages:
$ conda config –env –add channels conda-forge
$ conda install numpy
$ conda install matplotlib
$ conda install scipy
$ conda install opencv
$ conda install -c anaconda scikit-image
$ conda install -c conda-forge gdal