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GEP Live CD User Guide Last Update: 12/30/2015 GEP Live CD User Guide Wilson Leung Table of Contents Introduction ............................................................................................................................ 2 Acknowledgements .................................................................................................................. 2 Software Versions .................................................................................................................... 2 Questions about the GEP Live CD ........................................................................................... 2 Availability .............................................................................................................................. 2 Document History ................................................................................................................... 3 Download VirtualBox .............................................................................................................. 3 Install VirtualBox .................................................................................................................... 4 Install the VirtualBox Extension Pack ............................................................................................... 5 Using the GEP Live CD in VirtualBox ..................................................................................... 6 Download the GEP Live CD .............................................................................................................. 6 Create a new virtual machine ............................................................................................................. 6 Attach the GEP Live CD ISO image to the virtual machine .............................................................. 10 Add USB support to the virtual machine ......................................................................................... 11 Launch the GEP Live CD ................................................................................................................ 12 Shutdown the virtual machine ......................................................................................................... 14 Data persistence ..................................................................................................................... 15 Saving data to a USB Drive .............................................................................................................. 15 Saving data to a VirtualBox virtual hard drive .................................................................................. 16 Format the virtual hard drive .................................................................................................................. 16 Use the virtual hard drive as a persistent home directory ...................................................................... 19 Using the GEP Live CD Virtual Appliance in VirtualBox ...................................................... 21 Download the GEP VirtualBox Disk Image ..................................................................................... 21 Importing the Virtual Appliance ..................................................................................................... 21 Setup a shared drive between the host and guest systems .................................................................. 23 Create a mount point for the shared drive ............................................................................................. 25 Account Credentials for the GEP Live CD ............................................................................. 27 Additional Resources ............................................................................................................. 27 1 Last Update: 12/30/2015 Introduction The Phred/Phrap/Consed package is a powerful suite of tools designed for creating, editing and viewing genomic assemblies. However, despite recent improvements, installing the Consed package remains non-trivial and it requires the user to have some familiarity with UNIX systems. In addition, because Consed cannot run on Microsoft Windows, GEP faculty members might not be able to install the Consed package and incorporate sequence improvement into their curriculum. The Genomics Education Partnership (GEP) seeks to address these issues by providing a Live CD image with Consed already installed and configured for GEP projects. The Live CD can be used in many different configurations and settings: as a standalone bootable Live CD, a bootable Live CD inside a virtual machine, or an actual virtual machine in VirtualBox. In this user guide, we will focus on using the GEP Live CD and the GEP Live CD VDI virtual machine in VirtualBox on Windows 7. We decided to use Oracle VM VirtualBox because it runs on all three major platforms (Windows, Mac OS X, and Linux) and it is freely available. However, because all the major virtual machine programs (VMWare, Parallels, Virtual PC) support mounting ISO disk images, the Live CD should work on other virtualization platforms with only minor changes. In addition, the GEP virtual machine is also distributed as an Open Virtualization Appliance (OVA package), which is supported by most virtualization platforms. Acknowledgements • The GEP Live CD is based on the SliTaz GNU/Linux Live CD. For more information on SliTaz, please visit http://www.slitaz.org/en/. • Oracle’s VirtualBox software is available for download at http://www.virtualbox.org. Software Versions • GEP Live CD: version 4 • Operating System: Windows 7 SP1 • VirtualBox: Version 5.0.12 Questions about the GEP Live CD Please contact Wilson at [email protected] if you have any questions or encounter any problems with the GEP Live CD. Availability The GEP Live CD and the VirtualBox VDI is available for download at the GEP web site (http://gep.wustl.edu è Projects è Tools Under Development). 2 Last Update: 12/30/2015 Document History First Revision: 01/31/2011 Second Revision: 12/05/2012 Third Version: 08/07/2013 Current Version: 12/30/2015 Download VirtualBox In this user guide, we will setup VirtualBox to run a virtual machine on Microsoft Windows 7 SP1. Among the virtual machine software available, VirtualBox is the only one that can run on all three major platforms (Windows, Mac, and Linux) and is free for academic and personal use. To download a copy of VirtualBox, open a web browser and navigate to the VirtualBox home page at http://www.virtualbox.org and click on the “Downloads” link on the left navigation bar (Figure 1). Figure 1 Download VirtualBox from http://www.virtualbox.org Click on the link under VirtualBox platform packages to download the installer for your platform (e.g., VirtualBox 5.0.12 for Windows hosts). Click on the “All supported platforms” link under VirtualBox 5.0.12 Oracle VM VirtualBox Extension Pack to download the Extension Pack (Figure 2). For this tutorial, we will save these packages in the “MyPrograms” folder of your user account (e.g., C:\Users\Wilson\MyPrograms). Figure 2 Download installation package for your platform and the extension pack from the VirtualBox website. 3 Last Update: 12/30/2015 Install VirtualBox The steps required to install VirtualBox will differ depending on your platform. If you are on Windows, you will need to launch the installer using an account with administrative rights. Double-click on the VirtualBox installation package to launch the installer (Figure 3). Follow the instructions provided by the VirtualBox setup wizard to install VirtualBox (Figure 4). (Note that you might need to accept the installation of additional drivers from Oracle during the installation process.) Figure 3 Double click on the VirtualBox-5.0.12-104815-Win.exe file to launch the VirtualBox installer. Figure 4 Follow the instructions provided by the setup wizard to install VirtualBox. If all goes well, a message should appear indicating that installation was successful (Figure 5). Uncheck the box “Start Oracle VirtualBox 5.0.12 after installation” and then click “Finish”. 4 Last Update: 12/30/2015 Figure 5 Uncheck the “Start Oracle VM VirtualBox after installation” checkbox after installation is complete. Please refer to the Installation details section (https://www.virtualbox.org/manual/ch02.html) of the VirtualBox end-user documentation for details on specific installation issues for your platform. Install the VirtualBox Extension Pack While not required, we recommend installing the VirtualBox Extension Pack in order to enable support for external USB 2.0 and 3.0 devices. Go back to the File Explorer and navigate to the directory where you have downloaded the Extension Pack (e.g., C:\Users\Wilson\MyPrograms, Figure 6). Figure 6 Double click on the Extension Pack installer to add USB support to VirtualBox. Double click on the Extension Pack installation package. This will launch VirtualBox and a dialog will appear which asks us if we would like to install the Extension Pack. Click “Install” (Figure 7). Figure 7 Click on the "Install" button to install the Oracle VM VirtualBox Extension Pack. 5 Last Update: 12/30/2015 Using the GEP Live CD in VirtualBox Download the GEP Live CD After installing VirtualBox, we will setup a virtual machine to launch the GEP Live CD. The GEP Live CD is available for download on the GEP web site (http://gep.wustl.edu è Projects è Tools Under Development, Figure 8). Because of licensing restrictions for the Consed package, only members of the GEP can download the GEP Live CD. Please contact
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