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Installing BioLinux on Mac OS X or Windowsusing a virtual machine
Dr. Habil Zare, PhD
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Bio-Linux
Bio-Linux is a free workstation platform that facilitates running hundreds of bioinformatics tools without the corresponding installation hassles.
These guidelines will help you installing Bio-Linux from the provided flash drive on your Mac or Windows computer.
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Requirements
- A computer with at least 20 GB available space on the hard drive. A minimum of 4 GB of RAM is needed.
- The installation can take 10-20 minutes excluding the download time.
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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USB flash driveTo save time on installation, a USB drive is provided for the workshop. It contains the following files:
1. VirtualBox-5.0.8-103449-OSX.dmghttp://download.virtualbox.org/virtualbox/5.0.8/VirtualBox-5.0.8-103449-OSX.dmg
2. VirtualBox-5.0.8-103449-Win.exehttp://download.virtualbox.org/virtualbox/5.0.8/VirtualBox-5.0.8-103449-Win.exe
3. bio-linux-8-latest.ovahttp://nebc.nerc.ac.uk/downloads/bio-linux-8-latest.ova
Alternatively, you can download these files from VirtualBox and Bio-Linux, which may take several hours.
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 0: Close all your programs.
BioLinux needs extensive memory and CPU resources. Close all other programs unless you have a fast, high-performance computer.
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 1: Install VirtualBox Mac OS X
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 1: Install VirtualBox Windows
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 1: Install VirtualBox Mac OS X Windows
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 1: Install VirtualBox Mac OS X Windows
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 1: Install VirtualBox Mac OS X Windows
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 1: Install VirtualBox Mac OS X Windows
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 1: Install VirtualBox Mac OS X Windows
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 1: Install VirtualBox Mac OS X Windows
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 2: Run VirtualBox Mac OS X
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 2: Run VirtualBox The first time you run VirtuaBox, it looks like this:
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 3: Import BioLinuxMac OS X Windows
From the top menu, click on File>Import Appliance…
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 3: Import BioLinuxMac OS X Windows
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 3: Import BioLinuxMac OS X Windows
Use the bio-linux-8-latest.ova file from the USB drive.
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 3: Import BioLinuxMac OS X Windows
Make sure, in the next step, you will check
Reinitialize MAC address for all network cards.
Both Mac OS X and Windows
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 3: Import BioLinuxMac OS X Windows
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 3: Import BioLinuxMac OS X Windows
It can take 10-20 minutes ….
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 4: Turn on BioLinuxMac OS X Windows
Double-click on Bio-Linux to turn it on.
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 4.5: Enable VT-xWindows only
In Windows, you may get an error like this the first time you run Bio-Linux. To fix it, you need to enable Virtualization Technology (VT-x) by modifying BIOS, which is a little technical. Restart while pressing F2, F10, F12, or DEL.
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 4: Welcome to Linux world!Bio-Linux should appear after a black screen.
From this point on, there is not much difference between Mac OS X and Windows.
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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Step 4: Welcome to Linux world!Drag the bottom right corner of the screen to adjust
it to your convenience.
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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You are done!
- Bio-Linux is installed, and should work properly.
- You do not need the USB driver any more.
- Note that the above approach uses a virtual machine (VirtualBox), which is appropriate only for educational purposes and running simple tests by beginners. For more complicated analysis, installing Bio-Linux on a flash or hard drive is recommended to increase computation speed.
Instaling BioLinux using VM, Dr. Habil Zare 27 Oct 2015
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References:
• These guidelines were based on a blog post by Dave Lunt. http://www.davelunt.net/evophylo/2011/07/bio-linux-in-a-virtualbox/
• See the Bio-Linux website for documentation, training, and the list of supported software.http://environmentalomics.org/bio-linux/
• I prepared these guidelines to facilitate the “Bioinformatics for biologists workshop” to be held on 20 Nov 2015, UTHSC – San Antonio.http://oncinfo.org/Bioinformatics+for+biologist+workshop
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