# Bioinformatics: How to get your computer ready --- [TOC] ## Software We will use the software on RIT bioinformatic servers for most of our data processing and analyses. To interact with the servers you will need: 1. A terminal to connect to the servers 2. A program to transfer files from and to your computer What is a terminal? Find out [here](https://cs.colby.edu/maxwell/courses/tutorials/terminal/) https://cs.colby.edu/maxwell/courses/tutorials/terminal/ ![](https://i.imgur.com/drx87Fy.png) What is a file transfer program? Find out [here](https://en.wikipedia.org/wiki/FileZilla) https://en.wikipedia.org/wiki/FileZilla ![](https://i.imgur.com/IreN1qr.png) :::success How to connect in FileZilla * Open the new site icon (just under File) * Select ssh connection * Port 22 * Fill in the RIT connection data. ::: ## Install/Activate a terminal ### mac A full terminal, compatible with unix system is pre-installed. You can find detailed instructions for Mac users [here](https://support.apple.com/guide/terminal/open-or-quit-terminal-apd5265185d-f365-44cb-8b09-71a064a42125/mac). https://support.apple.com/guide/terminal/open-or-quit-terminal-apd5265185d-f365-44cb-8b09-71a064a42125/mac Useful shortcuts: to **copy and paste inside the terminal** use crt+shift+ c and crt+shift+ v :::warning thanks to Liuhao Wu, MAE 2020 As we realized in the class, most Mac users have default zsh terminal shells where * (asterisk) does not work, which causes issues when doing secure copying. The solution here is to switch from zsh shell to the bash shell and we might want to add this note to the tutorials for the future class. I am attaching the command lines I used to help them figure out below: * Type chsh -s /bin/bash on your LOCAL machine terminal * Then the terminal will prompt you to enter your Mac password * Quit the terminal and reopen that should make it work * We can also double-check if we're on bash shell now by typing echo $SHELL. If we get /bin/bash​, that means we are on bash shell and we can use * now! ::: ### windows Windows does not have a native terminal. You need to activate or install it. You can find detailed instructions on how to install an ubuntu terminal in win 10 [here](https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/). https://www.howtogeek.com/249966/how-to-install-and-use-the-linux-bash-shell-on-windows-10/ In brief, go here and activate the Windows Subsystems for Linux ![](https://i.imgur.com/oiB3Dq1.png) Now go to the store and download Linux, I recommend Ubuntu (e.g. 20.04 or 22.04) Useful shortcuts: how to find your files (your computer files) `cd /mnt/c` That is your C drive. Your files would be under Users, your username. How to **copy & paste** in the terminal in ubuntu in windows OS. By default, it might be set to use the right button of the mouse to paste after copying. I would recommend setting the terminal to use the same shortcuts the other students would be using. To do this in an open Ubuntu window click on the upper left corner, in the terminal app go to Defaults -> Check on Ctrl+Shift+C/V as Copy/Paste -> Click Ok. ### Linux If you are running Linux, you are probably pretty familiar with the terminal. If not, check [here](https://askubuntu.com/questions/38162/what-is-a-terminal-and-how-do-i-open-and-use-it). https://askubuntu.com/questions/38162/what-is-a-terminal-and-how-do-i-open-and-use-it To **copy and paste inside the terminal** use crt+shift+ c and crt+shift+ v ## secure file transfer You can use the scp command in the terminal to transfer files to and from your computer. This can be fast and efficient, or slow and confusing depending on what you're doing. You can find detailed info about transferring in this [unix tutorial](https://jbpc.mbl.edu/unix-tutorial/MAE2020.html#Copying_files_between_your_computer_and_the_server) https://jbpc.mbl.edu/unix-tutorial/MAE2020.html#Copying_files_between_your_computer_and_the_server It's worth installing a graphical interface that will let you move files around the way you're probably used to. We recommend FileZilla. ### FileZilla client Download the appropriate version of the program (**client version**) [Win64bit](https://filezilla-project.org/download.php?platform=win64) [Win32bit](https://filezilla-project.org/download.php?platform=win32) [MAC OSX](https://filezilla-project.org/download.php?platform=osx) [linux64](https://filezilla-project.org/download.php?platform=linux64) [linux32](https://filezilla-project.org/download.php?platform=linux32) webpage: https://filezilla-project.org/ ## text editor (Visual Code Studio) Copying commands from Word or other sophisticated word processors to the terminal leads to all sorts of problems. You'll want to use a simple text editor. One nice text editor is Visual Code Studio, which combines a folder-based interface and text edition capabilities. https://code.visualstudio.com/download It can be seamlessly integrated with the desktop version of [github](https://desktop.github.com/). Scripts and comments from this class can also be found on Github, https://github.com/elperedo/Microbiomes-Across-Environments ## Additional text editors. ### windows Windows has [Notepad](https://en.wikipedia.org/wiki/Microsoft_Notepad) ### mac Mac has [text edit](https://support.apple.com/guide/textedit/welcome/mac). Just follow the instructions [here](https://www.techjunkie.com/textedit-plain-text-mode/#:~:text=TextEdit%20opens%20a%20new%20document,in%20the%20TextEdit%20menu%20bar.) to make it plain text so that copying to the terminal goes smoothly. ### Linux you can use [text edit](www.gedit.org) from gedit. It is a small and lightweight text editor for the GNOME Desktop. ## Documenting your project It is important to store your code, so that 1. You (or anyone else) can repeat your analysis. 2. We can help you to troubleshoot any problem that you might encounter. This is part of your grading for this course. We will guide you through each analysis step, but we want you to document all the steps you took to arrive at your conclusions. We **strongly encourage you not to use** Word (.docx) or other sophisticated word processing programs to save your code. These programs embed many additional lines of code that will be misinterpreted by the terminal and the programs you will be using. Even "saving as" a text file may not remove all these symbols. :::success We recommend you use a text editor such as Visual Code or even websites such as this one, [HackMD](https://hackmd.io/) or [Github](https://github.com/) :::