Installing Conda, Setting Up Environments, and Installing Packages - statonlab/UTIA_Computational_Resource GitHub Wiki
Conda is an open source package and environment management. Within a conda environment you will be able to install any packages - and their dependencies - and run them. If you find a package that is unavailable in Spack but available in Conda, you can load a Conda environment and install the package.
There are multiple methods to install Conda; the simplest is to install the latest version of Miniconda. Miniconda is a simplified version of Anaconda containing only what is needed to run Conda. This can be set up in your home directory (~
).
cd ~
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
Complete the offered prompts, setting everything to default. Once installation is complete, close and reopen your window to confirm installation. If you are able to get a list of installed packages by running conda list
, Conda has been installed correctly.
Making a conda environment from scratch is fairly simple:
conda create --name <env_name>
conda activate <env_name>
I recommend making the name something you will be able to remember easily. If you aren't attempting to install packages that will conflict with each other, I also recommend creating one, centralized environment so that you know where most everything is located.
However, you may also need to load a saved environment associated with an existing package, such as aTRAM. This environment is created using the following commands:
cd /pickett_centaur/software/aTRAM
conda env create -f environment.yml
conda activate aTRAM
If you plan on running python for any bioinformatics pipelines, Biopython is essential. To install Biopython for use, activate your personal environment and run this command:
conda install -c conda-forge biopython
As long as your environment is active, you will be able to run biopython.
The -c
option specifies the channel from which we installed biopython, which will not be the same for every package you load. I recommend searching for your package + conda and getting the command from their documentation.