Oracle VM VirtualBox (formerly Sun VirtualBox, Sun xVM VirtualBox and Innotek VirtualBox) is a free and open-source hosted hypervisor for x86 virtualization, developed by Oracle Corporation.Created by Innotek, it was acquired by Sun Microsystems in 2008, which was in turn acquired by Oracle in 2010. VirtualBox may be installed on Windows, macOS, Linux, Solaris and OpenSolaris. For Windows guests, shared folders are implemented as a pseudo-network redirector. For Linux and Oracle Solaris guests, the Guest Additions provide a virtual file system. To share a host folder with a virtual machine in Oracle VM VirtualBox, you must specify the path of the folder and choose a share name that the guest can use to access the.
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With the shared folders feature of Oracle VM VirtualBox, you can access files of your host system from within the guest system. This is similar to how you would use network shares in Windows networks, except that shared folders do not require networking, only the Guest Additions. Shared folders are supported with Windows 2000 or later, Linux, and Oracle Solaris guests. Oracle VM VirtualBox includes experimental support for Mac OS X and OS/2 guests.
Shared folders physically reside on the host and are then shared with the guest, which uses a special file system driver in the Guest Additions to talk to the host. For Windows guests, shared folders are implemented as a pseudo-network redirector. For Linux and Oracle Solaris guests, the Guest Additions provide a virtual file system.
To share a host folder with a virtual machine in Oracle VM VirtualBox, you must specify the path of the folder and choose a share name that the guest can use to access the shared folder. This happens on the host. In the guest you can then use the share name to connect to it and access files.
There are several ways in which shared folders can be set up for a virtual machine:
- In the window of a running VM, you select Shared Folders from the Devices menu, or click on the folder icon on the status bar in the bottom right corner.
- If a VM is not currently running, you can configure shared folders in the virtual machine's Settings dialog.
- From the command line, you can create shared folders using VBoxManage, as follows:See Section 7.40, “VBoxManage sharedfolder”.
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There are two types of shares:
- Permanent shares, that are saved with the VM settings.
- Transient shares, that are added at runtime and disappear when the VM is powered off. These can be created using a checkbox in the VirtualBox Manager, or by using the
--transient
option of the VBoxManage sharedfolder add command.
Shared folders can either be read-write or read-only. This means that the guest is either allowed to both read and write, or just read files on the host. By default, shared folders are read-write. Read-only folders can be created using a checkbox in the VirtualBox Manager, or with the
--readonly
option of the VBoxManage sharedfolder add command. Oracle VM VirtualBox shared folders also support symbolic links, also called symlinks, under the following conditions:
- The host operating system must support symlinks. For example, a Mac OS X, Linux, or Oracle Solaris host is required.
- Currently only Linux and Oracle Solaris Guest Additions support symlinks.
- For security reasons the guest OS is not allowed to create symlinks by default. If you trust the guest OS to not abuse the functionality, you can enable creation of symlinks for a shared folder as follows:
You can mount the shared folder from inside a VM, in the same way as you would mount an ordinary network share:
- In a Windows guest, shared folders are browseable and therefore visible in Windows Explorer. To attach the host's shared folder to your Windows guest, open Windows Explorer and look for the folder in My Networking Places, Entire Network, Oracle VM VirtualBox Shared Folders. By right-clicking on a shared folder and selecting Map Network Drive from the menu that pops up, you can assign a drive letter to that shared folder.Alternatively, on the Windows command line, use the following command:While
vboxsvr
is a fixed name, note thatvboxsrv
would also work, replacex:
with the drive letter that you want to use for the share, andsharename
with the share name specified with VBoxManage. - In a Linux guest, use the following command:To mount a shared folder during boot, add the following entry to
/etc/fstab
: - In a Oracle Solaris guest, use the following command:Replace
sharename
, use a lowercase string, with the share name specified with VBoxManage or the VirtualBox Manager. Replacemountpoint
with the path where you want the share to be mounted on the guest, such as/mnt/share
. The usual mount rules apply. For example, create this directory first if it does not exist yet.Here is an example of mounting the shared folder for the user jack on Oracle Solaris:Beyond the standard options supplied by the mount command, the following are available:This option sets the character set used for I/O operations. Note that on Linux guests, if theiocharset
option is not specified, then the Guest Additions driver will attempt to use the character set specified by the CONFIG_NLS_DEFAULT kernel option. If this option is not set either, then UTF-8 is used.This option specifies the character set used for the shared folder name. This is UTF-8 by default.The generic mount options, documented in the mount manual page, apply also. Especially useful are the optionsuid
,gid
andmode
, as they can allow access by normal users in read/write mode, depending on the settings, even if root has mounted the filesystem. - In an OS/2 guest, use the VBoxControl command to manage shared folders. For example:As with Windows guests, shared folders can also be accessed via UNC using
VBoxSF
,VBoxSvr
orVBoxSrv
as the server name and the shared folder name assharename
.
Oracle VM VirtualBox provides the option to mount shared folders automatically. When automatic mounting is enabled for a shared folder, the Guest Additions service will mount it for you automatically. For Windows or OS/2, a preferred drive letter can also be specified. For Linux or Oracle Solaris, a mount point directory can also be specified.
If a drive letter or mount point is not specified, or is in use already, an alternative location is found by the Guest Additions service. The service searches for an alternative location depending on the guest OS, as follows:
- Windows and OS/2 guests. Search for a free drive letter, starting at
Z:
. If all drive letters are assigned, the folder is not mounted. - Linux and Oracle Solaris guests. Folders are mounted under the
/media
directory. The folder name is normalized (no spaces, slashes or colons) and is prefixed withsf_
.For example, if you have a shared folder calledmyfiles
, it will appear as/media/sf_myfiles
in the guest.The guest properties/VirtualBox/GuestAdd/SharedFolders/MountDir
and the more generic/VirtualBox/GuestAdd/SharedFolders/MountPrefix
can be used to override the automatic mount directory and prefix. See Section 4.7, “Guest Properties”.
Access to an automatically mounted shared folder is granted to everyone in a Windows guest, including the guest user. For Linux and Oracle Solaris guests, access is restricted to members of the group
vboxsf
and the root
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Oracle VirtualBox is a cross-platform virtualization application. It installs on your existing Intel or AMD-based computers, whether they are running Windows, Mac, Linux or Solaris operating systems. VirtualBox can create and run a 'guest' operating system (virtual machine) in a window of the host operating system. The virtual machine provides a self-contained environment in which to experiment with new software without risking damaging changes to the host operating system.
We will give an instruction with step-by-step screenshots to show how to install VirtualBox with an example of installing Ubuntu OS as a guest machine. We also explain how to share files between the host and guest operating systems.
Downloads
Note the instruction here is based on the latest version of the VirtualBox. If you have already installed an earlier version of VirtualBox, your experience may be different. It is recommended to use the latest version of VirtualBox to avoid issues. The VirtualBox forum is a good place to find a solution if you see any problems.
Go to VirtualBox website here to download the binary for your current operating system. Since our host machine is running on Windows, I'll choose 'x86/amd64' from Windows hosts. When download is finished, run the executable file. Continue with the installation of VirtualBox with the defaults. This will open VirtualBox at the end of the installation.
Create Virtual Machine
Click 'New' button to open a dialog.
Type a name for the new virtual machine. Since I am planning to install Ubuntu 14.04, I'll enter 'ubuntu1404'. Note that VirtualBox automatically changes 'Type' to Linux and 'Version' to 'Ubuntu (64 bit)'. These two options are exactly what we need.
The memory size depends on your host machine memory size. In my case, I have 12GB physical RAM. I like to allocate as much as possible for Ubuntu but leave some for my Windows host machine. I pick 8192 MB for my Ubuntu. Note that VirtualBox will create a swap partition with the same amount space as base memeory you have entered here. So later when you are selecting the size of the virtual hard drive, make sure it is large enough since the hard drive will be splitted into root (/)and swap partitions. The root partition contains by default all your system files, program settings and documents.
Accept the default 'Create a virtual hard drive now' and click 'Create' button.
Continue to accept the default 'VDI' drive file type and click 'Next' button.
Change the storage type from the default 'Dynamically allocated' to 'Fixed size' to increase performance.
For the virtual hard drive space, the default value is 8GB which is too little for RNA-Seq analysis. I'll pick 100GB since I have plenty of space in my hard disk. You want to choose a good size for your RNA-Seq analysis. If you realize the drive space is not large enough, you'll need to go over these steps again to create another virtual machine.
Click 'Create' button and VirtualBox will generate Ubuntu virtual machine.
Now the virtual machine is created. We are ready to install Ubuntu in this virtual machine. Select your new virtual machine and click 'Settings' button. Click on 'Storage' category and then 'Empty' under Controller:IDE. Click 'CD/DVD' icon on right hand side and select the ubuntu ISO file to mount.
Note that if you have not downloaded 64-bit Ubuntu ISO file, you can check out this page for more information. When downloading Ubuntu ISO file, make sure to selecte 64-bit version. Also make sure the VT-x/Virtualization Technology has been enabled in your computer's BIOS/Basic Input Output System.
Since Tophat program can take an advantage of multiple processors/threads, it is a good idea to specify a large number of processors in virtual machine (default value is 1). You can change this number by clicking on 'System' category. In this case, I change the number of CPUs to 4 since 4 is the largest value shown on the green bar in my case. Now you can click 'OK' button to continue.
VirtualBox may pop up a message about 'Auto capture keyboard' option. Read the message there and check 'Do not show this message again' option before clicking OK.
Install Ubuntu
Back to Oracle VM VirtualBox Manager, click on the new Ubuntu virtual machine and hit 'Start' button. Now you shall see a 'Welcome' screen. Click 'Install Ubuntu' button. Note that the installation process may differ a little bit from version to version. The screenshots here are based on Ubuntu 14.04.1.
Click 'Continue' button.
![Linux Linux](/uploads/1/2/6/4/126420041/723656458.jpg)
Make sure 'Erase disk and install Ubuntu' option is selected and click 'Install Now' button.
Ubuntu will ask you a few questions. If the default is good, click 'Continue' button.
In 'Who are you?' dialog, enter your preferred name, username and password. Note that this user will have root/sudo privilege. Click 'Continue' button.
The installation will continue until it is finished.
After installation is complete, click 'Restart Now' button. When you see a screen with a black background saying 'Please remove installation media and close the tray (if any) then press ENTER:', just follow it.
Enter the password you have chosen and press 'Enter'.
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The Ubuntu Desktop OS is ready. You may find the desktop screen is too small. Don't worry. You can solve this easily with 'VirtualBox Guest Additions'.
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Guest Additions
After the Ubuntu guest machine is installed, you will find the Ubuntu OS screen size is not extendable and you are not able to share folders between the host machine and Ubuntu.
Guest Additions software provide additional capability to a guest virtual machine, including mouse pointer integration, better video support, share folders, share clipboard, et al.
Before we proceed to install Guest Additions, make sure the current user has sudo/root privilege. If the current user does not have sudo/root privilege or it is not sure, run the following terminal command from an account (such as the user created when Ubuntu was first created; see the screenshot of 'Who are you?' above) with root privileges to enable the root privilege for the current user where USERNAME should be replaced by the current user's name.
To install Guest Additions, click Devices > Insert Guest Additions CD images…
Click 'Run' button (next to 'Cancel' button) to start the installation. Note that the version of VBOXADDITIONS should be matched with the one of VirtualBox you have installed.
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Installing Guest Additions requires root privilege. Enter user's password (assume the current user has sudo privilege).
When the installation is finished, press Return key to close the terminal window.
Now prepare to restart the system to enable the change. Click 'Shutdown' on the menu and then the 'Restart' button.
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After rebooting Ubuntu, you will see the desktop resolution is much better.
Share Folders
Before you can enable shared folders on the host machine, make sure you have installed VirtualBox Guest Additions software on the guest machine.
When Ubuntu guest machine is on, click on Devices > Shared folders settings…
Select Machine Folders and hit the add button (plus sign).
Browse to the folder you wish to access from the guest machine. Check Auto-mount and Make Permanent options and click OK button.
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Click OK button once more.
Now type 'terminal' in Dash to open a Terminal.
Type the following line in the Terminal to add a user to 'vboxsf' group. This step is necessary in order to use the VB's 'Shared Folder' feature.Replace 'brb' with your account name in Ubuntu.When you are done, restart the Ubuntu guest machine and go to /media/ directory. From Nautilus (file manager in Ubuntu), click Computer > File System > Media folder and inside it you will see a folder beginning with sf_ (the folder name is sf_Downloads in our example). Now you can transfer files between the Ubuntu guest machine and the Windows host machine in Nautilus.
Although Shared Folder system in VirtualBox is a nice feature, using VirtualBox shared folder directly for fastq data, annotation or output directorycan significantly reduce the performance compared to a native (Ubuntu) system or VirtualBox native system.
BRB-SeqTools
After Ubuntu has been successfully installed on VirtualBox, users can be go back to download and use BRB-SeqTools program.