---+ Computing Environment Setup %TOC% So, you want to harness the immense power of bioinformatics and computational biology for your science? Here are some things you probably want to think about in terms of your operating system, programs you want to download, and other tips for making things convenient. ---++ Minimum Setup In general, you'll need at least these things to get by in computation: 1 *Text Editor* – industrial strength, meaning it should have these features: * Show invisible characters (such as tabs) * Open and save files with different types of line endings (you'll want these to be Unix) 1 *Terminal* – for connecting to a Linux/Unix computer (your own or a cluster) 1 *SFTP File Transfer Program* – for transferring files back and forth to the computer On Macs, you can use these programs for the requirements: 1 [[http://www.barebones.com/products/bbedit][BBEdit]] (free for base features) 1 Terminal (built-in) 1 [[https://cyberduck.io/][Cyberduck]] (or you can use Terminal if you like typing scp commands) On Windows, you can use 1 ???? Not Notepad! 1 [[https://putty.org/][Putty]] 1 [[https://cyberduck.io/][Cyberduck]] On Linux: 1 1 1 But don't stop reading here... your life can be improved greatly by considering a few add-ons or alternatives/ ---++ Comfortable Setup ---+++ Getting an Authentic Linux Environment on Your Machine On Mac* and Linux systems, you will be able to run and test code on your own computer, which greatly speeds up and simplified development. *The Mac setup is not perfect at running all Linux tools. Occasionally some tools will not compile or run on Macs, but >95% of them work fine. To join the club on a Windows/PC machine, you can partition your hard drive and install Linux alongside your Windows install and boot one or the other. However, this has serious drawbacks in terms of splitting your hard drive space and not letting you use programs you are familiar with on Windows. Recently, it has become possible to use the [[https://learn.microsoft.com/en-us/windows/wsl/install][Windows Subsystem for Linux (WSL)]] to much more easily access a true Linux Environment. If you plan to write and run any code except maybe pure R scripts on your machine run computational pipelines and bioinformatics tools, you will want to install and use WSL. ---+++ Using an IDE A basic text editor is passable for changing config files and opening output files that don't play nice with Excel, but it is usually not very good for writing code. A true integrated development environment (IDE) typically offers these improvements: * Code formatting, syntax checking, and completion * Ability to step through your code for debugging * Integration with version control (e.g., git) The best IDEs depend a bit on what type of coding and activities you are doing: * VSCode (Mac and Windows versions) * Great for Python and other text files (including Markdown), has extensions for almost anything * As a bonus, you can connect to servers, edit files remotely, use it as a terminal for running commands, and browse files and perform drag-and-drop file transfer! * RStudio * Works great for all things R, including R markdown files, Shiny apps, etc. * XCode (Mac) * Meant for C++ coding. ---++ Deluxe Setup There are some advanced setup tricks that can save you a lot of time documented on other pages. These include: * Setting up SSH keys * Copying files with lftp to/from UT Box
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Topic revision: r1 - 2024-05-21 - JeffreyBarrick