forked from datacarpentry/genomics-workshop
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
removed libreoffice instructions; updated Windows command line etc. i…
…nstructions
- Loading branch information
Showing
1 changed file
with
13 additions
and
85 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -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:[email protected]) | ||
| 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 | ||
|
|
||
|
|
||