- Milan Malinsky – [email protected]
- Workshop Team
Short Amazon Web Services intro
For this workshop we are going to use a high performance cloud platform called Amazon Web Services (AWS). This is a flexible resource to get computational work done quickly and relatively inexpensively. We have set up individual AWS instances (virtual machines) for each participant. These have all the software and data you will need along with sufficient CPU, RAM, and storage resources. Your instance IP address can be found on this list here and the list of IP addresses is also liked from the main workshop page.
The IP addresses may change from time to time during the workshop, in case we need to install additional software, add datasets for exercises etc. We are going to announce if/when that happens.
Logging-in to your Instance
There are many ways to interact with a running virtual machine / instance. We shall be accessing the instance via programs that support SSH, X2Go and a web browser for some applications (e.g. R Studio).
Via the Terminal
For most of the workshop tutorials we recommend that you access the instance directly via a terminal program and the shell. This means text-only interaction with a UNIX-like system, which many of you are already familiar with. You will learn more about how to use the shell in the Unix tutorial. It is often the only way to run genomic analyses and interact with high performance compute clusters.
Open your favourite Terminal application and connect to your instance via ssh. In the command line below replace the XX-XXX-XXX-XXXs with your Instance IP address
Password: please see the whiteboard in the lab room.
Hint: Finding/Installing the Terminal
OS X comes preinstalled with an application called “Terminal”, you can search for it with Spotlight or in Finder.
All Linux distributions come with a terminal application. These may be in different places depending on what type of linux system you have. If you are using linux you probably already know how to find this; if not please ask one of the instructors for help.
Windows unfortunately does not have a terminal shell that would be useful for our purposes. However, there are several free options that we can use; we suggest PuTTY, which is a SSH terminal for Windows.
To download putty go to: http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html and select the version you want. In this case it should be “putty.exe”
After downloading the file, run it. In the Host Name bar insert the IP Address number for the Amazon Instance.
If this warning message appears, click “Yes”. This is a check that you trust the computer you are connecting to.
Then enter the username and the password and you are through to the terminal of your Amazon instance.
Via the X2Go software
For activities that require a Graphical User Interface (GUI), we can access our instance’s version of the desktop via a piece of software called X2Go (discussed below, with install instructions). This is probably going to be slower over the internet connection, another reason to use the shell terminal/ssh whenever we can. Also note that many other UNIX machines (e.g. your institution’s compute cluster) will not have the X2Go server installed as default and therefore you will not be able to connect using the X2Go client.
Hint: Installing X2Go client
We hope most of you have already done this (as suggested in an email from Scott Handley). If not, please follow the instructions below.
Prior to the installation of X2Go, you will have to install XQuartz (if you have not done it at home already). Download the dmg file at http://xquartz.macosforge.org/landing/. Then, to install X2Go, go to http://wiki.x2go.org/doku.php and click on the appropriate MacOS dmg for your computer to download. Open the .dmg file and move x2go into your Applications folder.
X2Go Client is part of Ubuntu 12.04 & later, as well as Debian Wheezy & Jessie. In Ubuntu, to install it you will probably need admin rights (sudo, root, etc.):
Open the terminal (Ctrl + Alt + T)￼
In the terminal, type sudo apt-get install x2goclient
Detailed instructions for other Linux flavours can be found in this link:
To start the X2Go client in Ubuntu (Linux), type x2goclient in the Terminal.
The link to install for Windows is here:
(If you do not have admin rights, alternative instructions can be found here http://wiki.x2go.org/doku.php/doc:installation:x2goclient)
Click on the latest link and select the setup program. Find this installer on your computer and execute it; you can keep the default values at each step of the installation. Once installed, you should have an X2go Client icon on your desktop which you can double click. When you first run the X2go Client, you may get a message about changes to your firewall. These changes are not necessary, so please just click “Cancel”.
After launching X2Go in your OS, you should see the main screen. (Note: on some versions of Windows you might get a security message. If so, please select “keep blocking”). Now you need to tell your computer where to connect to. If this is the first time you’ve opened X2Go, a new dialog will automatically pop up. If this is not the first time, then you’ll need to click on the “New session” icon.
Within the new session dialog box, you’ll need to specify:
– A session name: We recommend “WPSG 2018”.
– A host: Please enter the Public IP Address of your instance.
– A login: Please enter the username “wpsg”.
– The session type: Please select “MATE”.
When you click on OK, you should see something like the following.
Click on this, enter the password when prompted and press OK. The first time you connect to your instance you will be asked whether you “Trust the host”. Simply click next/yes to continue. Then after approximately 30 seconds, you should see the connection open. Congratulations! You’re now connected to your instance! It will look similar to below…