In case you want to be able to work locally on your computer (in addition to working at OSC, as we will in class), install the following free software packages.
For all operating systems:
VS Code: a text editor with a ton of functionality for coding and accessing remote computers.
Python: the main programming language used in this course.
For all Windows versions:
For Windows 10 only:
For Mac only:
(Because Mac and Linux users have a built-in Unix shell, and git for Windows ships with one, no-one should need to install a shell separately.)
Since all the software needed for this course is available at the Ohio Supercomputer Center (OSC), you are not required to install anything for this course. However, you may still want to install software locally so you are not completely dependent on OSC and don’t have to work inside a browser.
If you run into problems while installing software, please contact the instructors, but be aware that troubleshooting installation in Windows may be challenging for us.
Follow these instructions: Windows / Mac / Linux.
Follow the instructions at http://computingskillsforbiologists.com/setup/basic-programming/.
If you have Windows 10, I recommend installing WSL and then installing Git inside your Linux distribution in WSL (for instructions see the WSL section below), so you can skip the installation of Git for Windows. However, you may also want to version control directories outside of your WSL partition, in which case you should also install Git for Windows.
Download Git for Windows from here and install it using all the default settings for the installation, except:
In “Adjusting Your PATH Environment”, select “Use Git from Git Bash Only”.
In the prompt “Configuring the Line Ending Conversions”, choose “Checkout as-is, commit as-is”.
Follow these installation instructions Additional notes:
If you’re doing a manual installation or are otherwise prompted to pick a Linux distribution, I would recommend picking Ubuntu 20.04.
VS Code (which you installed earlier) has an integrated terminal, but this terminal will by default use a Windows shell. To tell it to use the bash shell from WSL instead:
Open the Command Palette (Ctrl + Shift + P)
Type “settings.json”, and open up the Settings (JSON) file.
Add this line: "terminal.integrated.shell.windows": "C:\\WINDOWS\\sysnative\\bash.exe"
Open a terminal in VS Code using “View” => “Integrated Terminal”, which should get you a bash shell after following the previous step.
Install Git by issuing the following command in the shell: sudo apt install git.
Open a terminal and enter: xcode-select --install.
Follow the instructions at https://brew.sh/.
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