Software Installs

Information on how to install some commonly used software and tools.

Bash

OS	Instructions
Windows	https://carpentries.github.io/workshop-template/#shell-windows
macOS	https://carpentries.github.io/workshop-template/#shell-macos
Linux	https://carpentries.github.io/workshop-template/#shell-linux

Conda (miniconda)

Install miniconda, not Anaconda.

This will also install Python, so if you wish to use a specific version of Python, you with want to specify that specific version when installing.

OS	Instructions
Windows	https://docs.conda.io/projects/conda/en/latest/user-guide/install/windows.html
macOS	https://docs.conda.io/projects/conda/en/latest/user-guide/install/macos.html
Linux	https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html

After closing and re-opening the terminal, the conda base environment should be enabled. To check this, make sure you see (base) to the left of your user name in the terminal prompt.

```
(base) user: $
```

Git

OS	Instructions
Windows	https://carpentries.github.io/workshop-template/#git-windows
macOS	https://carpentries.github.io/workshop-template/#git-macos
Linux	https://carpentries.github.io/workshop-template/#git-linux

Jupyter

I recommend installing through conda. See the conda install above first if you need to install conda, then follow the instructions below.

OS	Instructions
Windows	https://jupyter.org/install
macOS	https://jupyter.org/install
Linux	https://jupyter.org/install

Posit (formerly Rstudio)

OS	Instructions
Windows	https://posit.co/downloads/
macOS	https://posit.co/downloads/
Linux	https://posit.co/downloads/

Python

Python will also come installed with conda (depending on the installer that is used, I think). Choose the Python version that most of your packages will need. If you are unsure, I would start with Python 3.

OS	Instructions
Windows	https://realpython.com/installing-python/#how-to-install-from-the-full-installer
macOS	https://realpython.com/installing-python/#step-1-download-the-official-installer
Linux	https://realpython.com/installing-python/#how-to-install-on-ubuntu-and-linux-mint

R

OS	Instructions
Windows	https://rstudio-education.github.io/hopr/starting.html#how-to-download-and-install-r
macOS	https://rstudio-education.github.io/hopr/starting.html#how-to-download-and-install-r
Linux	https://rstudio-education.github.io/hopr/starting.html#how-to-download-and-install-r

Snakemake

I recommend installing this through conda. See the conda install above to first install conda, then follow the instructions below. I also recommend installing through mamba if possible.

OS	Instructions
Windows	https://snakemake.readthedocs.io/en/stable/getting_started/installation.html
macOS	https://snakemake.readthedocs.io/en/stable/getting_started/installation.html
Linux	https://snakemake.readthedocs.io/en/stable/getting_started/installation.html