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Installing Linux in a Virtual BoxWe will install a lightweight version of the Linux operating system called Xubuntu on your laptops. We will install the operating system within a VirtualBox, which behaves like a completely separate computer on your machine. The advantage of using a VirtualBox is that you can have the Linux operating system running in a window on your Windows machine and switch between Windows and Linux with the mouse. If you are interested in the different ways of running Linux under Windows then you can read more here: benefit of having Linux on your Windows machine is that it gives you access to a wide range of Bioinformatics software that is not available for Windows. However, software does tend to run more slowly within a virtual machine so if you want to do any intensive work on Linux then you may need a dedicated machine. The virtual machine will enable you to learn all the basics of Linux and run the exercises in this training course. There are several versions of Linux available. We are providing Xubuntu which is a lightweight version of Ubuntu which works well within a virtual machine and should not take up too much space on your computer. Ubuntu is also one of the most widely used versions of Linux for PCs and therefore has plenty of online support. However Biolinux is a version of Ubuntu which comes bundled with over 250 Bioinformatics software packages that you might like to try if you want to explore Linux further the course software there is a Xubuntu clone with all the course software preinstalled. However should you ever want to install another operating system in a VirtualBox instructions for doing so are in the document “Installing xubuntu in a virtual box from scratch.docx” and on the web.VirtualBox and Xubuntu for 64bit Windows machines are available in the course software. You can download them from here Xubuntu-16 file is big (~3Gb) and but should download quite quickly form the ILRI server. If you have a 32bit machine you will need to download the software yourself and do a separate installation. Ask for instructions but it will be much more complex than installing the 64-bit virtual machine that I have prepared. If you have a mac you will need the VirtualBox dmg in the course software but the Xubuntu VirtualMachine is the same and the instructions are the same.I obtained VirtualBox for Windows from the VirtualBox and Xubuntu software to your PC. Unzip the xubuntu-16.zipDouble click the VirtualBox-5.1.14-112924-Win.exe and follow the instructions. You can accept the defaults for all options. If you are having trouble there are sets of instructions here: here: you have installed VirtualBox you will need to Create a new Virtual machine (VM) Click the Blue sun symbol which says “New”. In the first dialogue set Name: xubuntuType: Linux (from the drop down list)Version: Ubuntu (64 bit) (from the drop down list)Click Next and then set the amount of Memory to 2Gb provided you have at least 4Gb on your machine. If not leave it at 1GbHard Disk. Select “Use an Existing Hard Disk” and click the icon to the right of the drop down back to browse for xubuntu-16.vdi withint the xubuntu-16 folderSharing Folders Once you have restarted Ubuntu you should create a shared folder for all your course work. If you do not already have a folder for the course work on your windows machine create one now.To access the folder that is shared between linux and windows you need to install more software:On the Xubuntu window:Now we need to install some additional software from to make the folder visibleDevices->Insert Guest Additions CD imageMost work in Linux is done from a terminal window. To continue open a terminal window using Alt-F1 or right click on desktop and select “Open Terminal Here”Remember that Linux is case sensitive so you must use capitals and lower case exactly as shown in these commands. Also Linux does not handle spaces in file names very well so it is best to avoid them. However if you have to have them then you will need to put a “\” before each space. Eg “Course Folder” would have to be entered as “Course\ Folder”. So in this case it would be preferable to call the folder “CourseFolder”.Commands to type into the terminal are shown in Courier fontIf you have to change a name for your system it will be shown in italicsChange directory (cd) to the folder where software has been copiedcd /media/VBOXADDITIONS_5.1.14_112924on some systems it might be cd /media/harry/VBOXADDITIONS_5.1.14_112924Install the software. sudo means do as super user or administrator and allows you to install software. It will ask for the password which is ilri2017sudo ./autorun.shNow we have the necessary software you can select the folder to link toDevices->Shared Folders->Shared Folder SettingsClick on the “Plus Sign On a Folder” image on the left of the window to create a new shared folder. Click on the drop down box for folder path and navigate to your course folder and select it. Check the Make-permanent and Auto-Mount boxes.OKOKGo to your Documents folder. “~/” means your “home directory” where you should keep all your files.cd ~/Documentsget a list (ls) of files in your Documents folderlsThere should be a folder called eucalypt which is, an arbitrary name for the mountpoint where the shared folder will be located and we will be doing some exercises on data from eucalyptus. Now we can mount (attach) the “SharedFileName” folder on your windows machine and attach it to the eucalypt directorysudo mount –t vboxsf SharedFileName eucalyptTo check if this has worked list the contents of the “eucalypt” folder:cd ~/Documents/ls eucalyptYou should get a list of all the files in your course folder on the windows machine.Copy and Paste between windows and linuxTo enable copy and paste between windows and linux:Select (Highlight) the xubuntu machineSettings->General->Advanced->Share Clipboard->BidirectionalLearning LinuxThere is a useful set of short introductory tutorials for Linux prepared by the University of Surrey UK at doing the Tutorials 1-6 this evening. ................
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