Contents.Before you jump into this tutorialThese are a few points that you should know before you start this tutorial:. Linux is re-coded under an open-source licence, the same way as R is a re-coded version of S. Here, when I use the term Unix, I refer to all Unix-like computing environments, i. The original Unix that comes with Macs as well as most Linux flavours.

Erik Eckel introduces Mac Terminal and defines some basic functionality that will help users learn to take advantage of its efficiency. Mac Terminal basics: Unlock the power of the command.

This tutorial was originally designed to be run on the computer cluster of the University of Sheffield called. However, if you cannot access iceberg, then access the compute cluster or desktop compute server at your own institute (assuming that they have some kind of Unix installed, of course). The section might still be helpful for that. Iceberg has scientific Linux and the job scheduling programme installed.

If you have an iceberg account, you will log into that account on Iceberg. If you don't have an iceberg account yet, either before you start this tutorial or begin this tutorial on any Linux/Unix machine, remotely or locally. All tasks of this and the can be done on any Unix/Linux machine (with the only exception of the second part of the second to last task in the advanced part of this tutorial that will show you how you can exploit a computer cluster for your work). The section contains two parts: one for users with iceberg access and a second for those without.

This tutorial expects you to do all the steps exactly as written from top to bottom. So refrain from experimenting during the first run through it to avoid unnecessary frustration. This tutorial is designed to be a guided tour through the world of Unix for you as a biologist. However, it does not explain everything in full detail. Frankly, that would be too boring for me to write down! Instead, it frequently expects from you to make sense of the output from a command and thereby infer what this command just did.

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Now that you know this, I am sure you won't be easily stumped by anything in this tutorial. Your command line prompt will end with a $ sign. So a $ sign in this tutorial tells you to type the stuff that comes after the $ sign into your command line and then press ENTER/ RETURN in order to execute that command line. You will see error messages! I still see them everyday that I use the Unix command line. And at the beginning almost all of them are caused by small and sometimes not very obvious typo's. So when you see an error message, the first thing you should do is check for typo's.

To do this, press the Up-arrow key on your keyboard which brings back the last command you executed and let's you edit it. The words 'folder' and 'directory' mean the same thing. So I use them interchangeably.

Please refrain from just copy-pasting commands from this tutorial into your command line! I strongly believe that this would lead to a bad learning outcome. On the one hand, you need to practice typing commands. It may feel awkward at the beginning, but believe me you will soon get faster and faster at it. On the other hand, typing in those command lines forces you to look carefully and pay attention to detail. It should also help you remembering more of these commands in the future, although you can always come back to this tutorial to refresh your memory. Another reason for typing instead of copy-pasting is occasional unintended formatting of text of command lines in this tutorial (I am trying to weed that out).

For instance, it appears that sometimes curly quotes - “ - have slipped into command lines in this tutorial instead of the straight quotes - ' - that you should find on your keyboard. Unsurprisingly, this will lead to errors. I often see people going through this tutorial having part of their screen with the window of the Internet browser and another with the window of their terminal programme. They then use their mouse when they need to make the other window active. This is not optimal. You should have all your windows using the whole screen, i. The currently active window covering all other windows that are open.

On Mac you can then use the Cmd + TAB key combination or on Linux the Ctrl + TAB key combination to easily switch to another window. Have a look at this little. This is a much faster way to switch between windows and allows you to use your whole screen for each window that you have open.

There are still small (hopefully not large) bugs lurking in this protocol. Please help to improve it by correcting those bugs or adding new tasks, more or better explanations and writing comments on the. Is easy and allows you to edit pages or create new ones just like on Wikipedia.Iceberg - making first contact from WindowsOpen in a new browser tab.On the new page, follow the link Access via a web browser. You should then see the following:There, click on Connect via myApps Portal, which should open a login site in a new browser tab:Insert the username/login name and password that you have been given by the administrators of the workshop.After you log in for the first time you may see a Java warning. Click on 'Activate Java', choose 'Allow and remember' from the drop-down menu, click 'Ok'.A pop-up box will prompt you to run the Oracle Secure Global Desktop Client, then click 'Yes' whan asked if you wish to connect to the server.Under Iceberg Applications select Iceberg terminal.A new window will pop up.Iceberg access for Mac and Linux usersOpen a terminal, then type at the command line prompt:$ ssh -X yourusername@iceberg.shef.ac.ukYou will be asked for your iceberg password and at the first time it usually issues a warning about accessing an untrusted server.

Just confirm that you want to add iceberg to your trusted server connections. The -X switch opens a connection with forwarding. If you don’t intend to open a on iceberg, skip that switch.Some basicsOn the head node called iceberg1 or iceberg-login1 start a new session on one of the worker nodes by typing:$ qshPlease be aware that no work should ever be done on the head node called iceberg1 or iceberg-login1!

This node is just a gateway to the worker nodes. You can see the name of the node you are on in your command line prompt.If you’ve logged in via the web browser or from a Unix/Linux terminal window via ssh -X and used qsh (instead of qrsh) to start a new session, then you can open a programme that uses a graphical user interface (GUI), e. Try it out now!$ firefoxAs a side note: if you had logged in via a programme called PuTTY, you would not be able to open graphical user interfaces remotely without installing further programmes (e. Exceed).So where are you now in the file system?$ pwdHere is a visual representation of a Unix file system:taken from theEvery Unix operating system has a root folder simply called /. Let’s see what’s in it using the command to list information about files.

Please note that the command uses the lower case letter 'l', not the number '1':$ ls /List the files in the current directory, i.