Installing and Running Bio-Linux
This page contains the following sections:
- Booting Bio-Linux from USB or DVD
- Installing Bio-Linux directly to your hard drive
- Running Bio-Linux as a VM with VirtualBox
- Upgrading Bio-Linux 7 (or Ubuntu 12.04/14.04) to Bio-Linux 8
- Troubleshooting FAQ for booting and installation
Note – Bio-Linux 8 is based on Ubuntu 14.04 desktop release. The boot loader, system kernel and installer are unmodified. Therefore any instructions pertaining to Ubuntu 14.04 also apply to Bio-Linux. You should make use of the extensive Ubuntu documentation in addition to this brief guide.
Booting Bio-Linux from USB or DVD
The ISO file format can be recorded directly to DVD media using your regular DVD burning software. Ensure you use the burn from image or equivalent option. If you simply save the ISO file to a disc then the result will not be bootable.
Likewise, just copying the file to a USB stick will not make it bootable. A simple cross-platform way to create a bootable USB stick is UNetBootin. Just follow the instructions that come with the software. You can choose whether or not to enable persistent storage on the stick.
There is also a USB maker tool in Bio-Linux, which can be run as “sudo bio-linux-usb-maker” from the command line. This is useful for making batches of multiple sticks, which can be great for demos and courses.
Whichever option you choose, you will need to get the computer to boot from the medium directly. How to do this varies from machine to machine – you may need to edit the BIOS settings or to press a key (F12 on Dell machines) during boot-up. Ubuntu 14.04 is designed to boot on Windows 8 UEFI machines but some particular machines make this awkward so you may need to experiment and/or consult the Ubuntu forums. Note – most Apple Mac computers will not boot from Bio-Linux USB sticks and this is something we cannot easily fix.
Upon booting, you will be given the option to “Try” or “Install” Bio-Linux. The latter option starts the installer but will not modify your hard drive until you have set specified partitioning preferences.
Installing Bio-Linux directly to your hard drive
Bio-Linux can install itself either as the sole operating system or side-by-side with Windows. In the latter case you will need to choose which system to use each time you boot. If you have enough RAM available then the VM option below may be better.
*** Important! Important! Important! Important! ***
Repartitioning your drive always carries a risk of data loss. Back up your system fully before installing Bio-Linux. Neither we nor the Ubuntu developers can accept any responsibility for loss of existing data caused by installing Bio-Linux.
Once you have the DVD or USB booted, and select “Install Bio-Linux”, a graphical installer wizard guides you through installation. The process starts with some simple choices of your time zone and keyboard layout, then ask about partitioning. If you go for a dual-boot setup you will have the option to specify how space is split between Linux and Windows. Note that you can access files from across the systems but things like installed Linux software need to live on the Linux disk, so assigning at minumum 40GB is recommended.
You are prompted to create an initial account during the installation process. This account will automatically be given administrative privileges, such as the ability to change system settings in the Control Centre and to obtain a root shell with “sudo -i”. Any further accounts will be created by this initial user once the system is installed. Use a secure password for this user – by default the account is set up with remote access via SSH/x2go enabled and is thus vulnerable to hacking.
Once the installation process is complete, you will be prompted to reboot your computer. At this point, don’t forget to remove the DVD or USB stick so it doesn’t boot again.
After logging in to your new system, Please refer to the Bio-Linux Userguide (available on your Bio-Linux desktop) and the tutorials also found there.
A note on setting up your network…
By default, the system assumes it will be able to obtain an IP address automatically (via DHCP) and to connect directly to the internet for web access. If you have static IP address you will need to ask your local IT admin for it. Likewise many sites have a mandatory web proxy which you will need to specify or else web pages will not be accessible (since system updates also work via web requests this is really important). See the Userguide for how to set these things up.
Running Bio-Linux as a VM with VirtualBox
VirtualBox is a free and powerful cross-platform VM manager found at http://virtualbox.org. The OVA file is designed for use with this system but should also work with similar systems like VMWare and Parallels.
⚠ Bio-Linux is a 64-bit operating system. Virtually all modern PC processors support 64-bits, even if you have 32-bit Windows installed. As a rule of thumb, if you have more than 1 processor core you will have 64-bit support. You may need to modify BIOS settings. See: https://www.virtualbox.org/manual/ch03.html#intro-64bitguests
Setup for VirtualBox:
- Ensure you have at least 40GB free disk space.
- Download and install the appropriate version of VirtualBox from the link above.
- Download the OVA file.
- Start VirtualBox and select Import Appliance from the File menu and import the .ova file (don’t worry that it says you need an OVF file).
- When importing the appliance, select the option to reinitialize the MAC addresses of network cards.
- Start the VM and if you see a log-in screen, log in as user manager with password also manager.
- Once this is working, you can delete the .ova file to save space.
- See the VirtualBox docs for more details including how to share folders and hardware. You will also want to adjust hardware settings such as CPU, RAM and video acceleration settings to suit your hardware.
You should treat the VM as a real machine for security purposes and apply all system security updates in a timely manner. The default manager password is, clearly, not secure. This might not be a problem because by default nobody can access the Linux VM unless they have direct access to your computer, but if you open up the network settings (eg. by adding port forwarding rules) then you must secure the account with a strong password or else take other steps to limit remote access. Ideally enforce key-only access via SSH.
Upgrading Bio-Linux 7 (or Ubuntu) to Bio-Linux 8
Ubuntu has an updater system that upgrades from one release to the next. This is closely related to the system that installs software and keeps it updated – it all uses the DPKG package manager under the hood. Bio-Linux also has an updater system that partly invokes the Ubuntu updater and partly adds its own stuff. It first ensures that the base Ubuntu has been updated to 14.04 and then brings in the Bio-Linux packages and look-and-feel as well as x2go etc.
If you have Bio-Linux 7…
Open a terminal as an administrative user (one who can use sudo) and run this command:
Follow the instructions. In the normal case, upgrade8.sh will run the Ubuntu upgrader for you to get you to Ubuntu 14.04, then instruct you to reboot and to run upgrade8.sh a second time to finish the job.
If you have Ubuntu 14.04…
You can use the same script, but you probably don’t have the runurl command so use this equivalent invocation:
wget -qO- http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh | sudo sh
If you have some earlier Ubuntu version…
Upgrade to Ubuntu 14.04 by following the regular Ubuntu upgrade process, then once you have that working, run the script as above. This should also work for Bio-Linux 6, if for some reason you still have that.
Problem: I can’t get Bio-Linux USB/DVD to boot on a Mac
Bio-Linux will not boot from a Live USB stick in most Mac computers, though some have reported the newer models work. Some Macs will boot the DVD but others will not. In any case, the installer does not have the option to set up dual-boot on the Mac as you need to do it via Bootcamp. The most reliable approach is to download the OVA and run it via Parallels or VirtualBox. Don’t forget to check the file integrity as detailed below.
Problem: I suspect the ISO (or OVA) file didn’t download properly
It is very simple to check that the file you downloaded has not been corrupted, as we provide an md5sums file for all the downloads on the site. On Linux give these two commands:
md5sum -c md5sums.txt
You’ll see errors for all the missing files, but look for a line regarding the ISO file, like this.
If the checksum is OK, you can be fully confident that the download worked.
To use the md5sums on other platforms, including Windows, try this application: http://jsummer.sf.net
Problem: My DVD won’t boot at all
You need to ensure that you used the “Burn from image” or “Make from ISO” or similar option on the recorder software. To check this, insert the DVD into the computer and look at the files on it. You should see a selection of about 12 files and folders. If you only see the original ISO file then you did not use this option and the DVD will not be bootable.
If the files appear, it may be that the DVD didn’t quite record properly. Errors on discs are common. If your DVD burner software has a disc integrity verification feature, you should use this. Also, try booting the disc in another machine before blaming the disc.
Problem: My Bio-Linux DVD only boots part way, then crashes
The first menu you see upon booting offers an option to verify the disc contents. This is done by using internal check-summing with the md5 system mentioned above. If the verification succeeds then the disc is good, and there is probably a compatibility issue with the system on your machine. If it produces any errors at all the DVD is broken and is not going to boot.
Problem: I installed Bio-Linux but it doesn’t boot up from the hard drive
The last bit of the installation process installs a thing called the “GRUB bootloader” which is in charge of starting Linux. Sometimes this bit fails. You can try re-running the installer as it has a repair mode to help you fix this and similar issues.
Problem: I want to remove Bio-Linux and revert my dual-boot system back to Windows
(Really, not the other way around??) There is no simple uninstaller tool. The simplest option is to just remove the Linux partition from within Windows, but you also need to restore the Windows bootloader in place of GRUB or the PC will not boot. A good guide is here.
Problem: I can’t find Wubi on the DVD
Due to many problems with Wubi and user misunderstandings of what it does we’ve removed it from the release. If you really want a Wubi system the option of installing Ubuntu 14.04 and adding Bio-Linux to it is open to you.
Getting more help
We endeavour to assist anyone struggling with Bio-Linux, so please contact us via the Bio-Linux mailing list address if you are unable to get Bio-Linux working.