diff --git a/learners/setup.md b/learners/setup.md index c7fcb646..9f330678 100644 --- a/learners/setup.md +++ b/learners/setup.md @@ -5,31 +5,22 @@ title: Setup # Overview This workshop is designed to be run on pre-imaged Amazon Web Services (AWS) instances. -All of the data and most of the software used in the workshop are hosted on an -Amazon Machine Image (AMI). -Some additional software, detailed below, must be installed on your computer. +We will be providing you with an AWS instance. To access your AWS instance, some additional software, detailed below, may need to be installed on your computer. -Please follow the instructions below to prepare your computer for the workshop: - -- Required additional software + Option A - **OR** -- Required additional software + Option B ## Required additional software -- This lesson requires a working spreadsheet program. **If you don't have a spreadsheet program already**, you can use LibreOffice, which is a free, open source spreadsheet program. Directions to install are included for Windows, Mac OS X, and Linux systems below. +- This lesson requires a working spreadsheet program. If you have a working spreadsheet program installed on your computer, such as Microsoft Excel or [LibreOffice](https://www.libreoffice.org/) (a free, open source spreadsheet program), you can use that. Otherwise, you can use Google Sheets. Either option will work well for this workshop. - For Windows, you will also need to install either Git Bash, PuTTY, or the Ubuntu Subsystem. Instructions are below. :::::::::::::::: spoiler -## Windows +## Windows users only: Setting up software you can use to connect to your cloud computer + +Open your Command Prompt app by searching for "cmd". At the command prompt, type `ssh`. Confirm that this prints out the usage information for the `ssh` command. If the result is "Command not found" then you have a few options: -- **If you already have a spreadsheet program such as Microsoft Excel, you can skip this step.** If you *don't* have a spreadsheet program, visit [the LibreOffice installation page](https://www.libreoffice.org/download/libreoffice-fresh/). - The version for Windows should automatically be selected. - Click Download Version X.X.X (whichever is the most recent version). - You will go to a page that asks about a donation, but you don't need to make one. - Your download should begin automatically. Once the installer is downloaded, double click on it and LibreOffice should install. -- Next, download the [Git for Windows installer](https://git-for-windows.github.io/). +- Set up the Ubuntu Subsystem for Windows. This option is only available for Windows 10 - detailedinstructions are available at [https://docs.microsoft.com/en-us/windows/wsl/install](https://docs.microsoft.com/en-us/windows/wsl/install). +- Download the [Git for Windows installer](https://git-for-windows.github.io/). Run the installer and follow the steps below: - Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens. @@ -53,78 +44,15 @@ Please follow the instructions below to prepare your computer for the workshop: - Click on "Install". - Click on "Finish". - Check the settings for you your "HOME" environment variable. - - If your "HOME" environment variable is not set (or you don't know what this is): - - Open command prompt (Open Start Menu then type `cmd` and press [Enter]) - - Type the following line into the command prompt window exactly as shown: `setx HOME "%USERPROFILE%"` - - Press [Enter], you should see `SUCCESS: Specified value was saved.` - - Quit command prompt by typing `exit` then pressing [Enter] -- An **alternative option** is to [install PuTTY](https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html). - For most newer computers, click on putty-64bit-X.XX-installer.msi to download the 64-bit version. - If you have an older laptop, you may need to get the 32-bit version putty-X.XX-installer.msi. - If you aren't sure whether you need the 64 or 32 bit version, - you can [check your laptop version](https://support.microsoft.com/en-us/help/15056/windows-32-64-bit-faq). - Once the installer is downloaded, double click on it, and PuTTY should install. -- **Another alternative option** is to use the Ubuntu Subsystem for Windows. - This option is only available for Windows 10 - the Microsoft documentation provides - [detailed instructions for installing Windows 10](https://docs.microsoft.com/en-us/windows/wsl/install-win10). - -::::::::::::::::::::::::: - -:::::::::::::::: spoiler - -## Mac OS X - -- **If you already have a spreadsheet program such as Microsoft Excel, you can skip this step.** If you *don't* have a spreadsheet program, visit [the LibreOffice installation page](https://www.libreoffice.org/download/libreoffice-fresh/). - The version for Mac should automatically be selected. - Click Download Version X.X.X (whichever is the most recent version). - You will go to a page that asks about a donation, but you don't need to make one. - Your download should begin automatically. Once the installer is downloaded, double click on it and LibreOffice should install. - -::::::::::::::::::::::::: - -:::::::::::::::: spoiler - -## Linux - -- **If you already have a spreadsheet program such as Microsoft Excel, you can skip this step.** If you *don't* have a spreadsheet program, visit [the LibreOffice installation page](https://www.libreoffice.org/download/libreoffice-fresh/). The version for Linux should automatically be selected. - Click Download Version X.X.X (whichever is the most recent version). - You will go to a page that asks about a donation, but you don't need to make one. - Your download should begin automatically. Once the installer is downloaded, double click on it and LibreOffice should install. + - If your "HOME" environment variable is not set (or you don't know what this is): + - Open command prompt (Open Start Menu then type `cmd` and press [Enter]) + - Type the following line into the command prompt window exactly as shown: `setx HOME "%USERPROFILE%"` + - Press [Enter], you should see `SUCCESS: Specified value was saved.` + - Quit command prompt by typing `exit` then pressing [Enter] +- Another option is to install the MobaXterm desktop app. Please follow the download instructions at [mobaxterm.mobatek.net](https://mobaxterm.mobatek.net/){:target="\_blank"} to download the free edition. ::::::::::::::::::::::::: -## Option A (**Recommended**): Using the lessons with Amazon Web Services (AWS) - -If you are signed up to take a Genomics Data Carpentry workshop, -you do *not* need to worry about setting up an AMI instance. -The Carpentries staff will create an instance for you and this will be provided to you at no cost. -This is true for both self-organized and centrally-organized workshops. -Your Instructor will provide instructions for connecting to the AMI instance at the workshop. - -If you would like to work through these lessons independently, outside of a workshop, -you will need to start your own AMI instance. -Follow these [instructions on creating an Amazon instance](https://datacarpentry.org/genomics-workshop/AMI-setup). -Use the AMI `ami-04dd77cd58b3ec654` (Data Carpentry Genomics with R 4.2) -listed on the Community AMIs page. -Please note that you must set your location as `N. Virginia` in order to access this community AMI. -You can change your location in the upper right corner of the main AWS menu bar. -The cost of using this AMI for a few days, -with the t2.medium instance type is very low (about USD $1.50 per user, per day). -Data Carpentry has *no* control over AWS pricing structure and provides this -cost estimate with no guarantees. -Please read AWS documentation on pricing for up-to-date information. - -If you're an Instructor or Maintainer or want to contribute to these lessons, -please [get in touch with us](mailto:team@carpentries.org) -and we will start instances for you. - -## Option B: Using the lessons on your local machine - -While not recommended, it is possible to work through the lessons on your local machine -(i.e. without using AWS). -To do this, you will need to install all of the software used in the workshop -and obtain a copy of the dataset. -Instructions for doing this are listed below. ### Data