NeuroDebian Virtual Machine
===========================
+`Installation`_ | `Working with the virtual machine`_ | `Troubleshooting`_ |
+`What has changed`_
+
.. quotes::
:random: 1
:tags: vm
-For those who are not yet running a Debian-based operation system we offer a
-`virtual machine`_ that can be used with `VirtualBox`_, allowing users to benefit
-from a Debian-based research environment on other operating systems.
-This virtual machine initially comes as a compact Debian installation that can,
-once installed, be equipped with a large variety of neuroscience software with
-just a few mouse clicks (e.g. AFNI_, Caret_, FSL_, PyMVPA_).
+For all systems running a non-Debian-based operation system, such as MS Windows
+or Mac OS X, we offer a `virtual machine`_ that can be equipped with a large
+variety of neuroscience software with just a few mouse clicks (e.g. AFNI_,
+FSL_, PyMVPA_).
.. _virtual machine: http://en.wikipedia.org/wiki/Virtual_machine
-.. _AFNI: http://afni.nimh.nih.gov/afni/
-.. _Caret: http://brainvis.wustl.edu/wiki/index.php/Caret:About
-.. _FSL: http://www.fmrib.ox.ac.uk/fsl/
-.. _PyMVPA: http://www.pymvpa.org
-
-
-Downloads
----------
-
-* `NeuroDebian 6.0.6 image (32bit)
- <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_i386.ova>`_ [~559MB]
-
- *This image should work on virtually all systems that are supported by*
- VirtualBox_ *and can be used whenever the, otherwise preferable, 64bit image
- is not compatible with a host machine.*
-
-* `NeuroDebian 6.0.6 image (64bit)
- <http://neuro.debian.net/debian/vm/NeuroDebian_6.0.6_amd64.ova>`_ [~576MB]
-
- *This image only works on 64bit host machines with active hardware
- virtualization support. The should include all recent Apple hardware and most
- 64bit Windows systems.*
-
-Virtual appliances above carry guest additions for 4.x series of the
-VirtualBox. If you still have VirtualBox 3.x, use previous 6.0.2
-virtual appliances:
-
-* `NeuroDebian 6.0.2 image (32bit)
- <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
-
-* `NeuroDebian 6.0.2 image (64bit)
- <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
-
-.. note::
-
- This older virtual appliances are distributed as a `zip` file. Please
- extract all files from the `.zip` file, using appropriate software
- for your operating system.
-
-.. note::
-
- You can verify that you have downloaded archives correctly using
- `md5sums -c MD5SUMS
- <http://neuro.debian.net/debian/vm/MD5SUMS>`_ . You can also verify
- the authenticity of the `MD5SUMS
- <http://neuro.debian.net/debian/vm/MD5SUMS>`_ itself using `gpg
- --verify MD5SUMS.gpg
- <http://neuro.debian.net/debian/vm/MD5SUMS.gpg>`_ signed with
- NeuroDebian archive key.
-
-* `VirtualBox download page <http://www.virtualbox.org/wiki/Downloads>`_ (Windows, Linux, Mac,
- Solaris)
-
- *This webpage offers installers of the VirtualBox application, as well as the
- documentation.*
-Changes
--------
-
-6.0.6 -- 01 Oct 2012
-
- * Updated core system to Debian squeeze 6.0.6
-
-6.0.5 -- 10 Nov 2011
-
- * Updated core system to Debian squeeze 6.0.3
- * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
-
- - ``~/host`` is now symlinked to correct path ``/media/sf_host``
- - ``brain`` user is added to ``vboxsf`` group so mounted host
- directories should become readily available
-
- * Root partition size and swap space got doubled in size (40GB
- and 2GB correspondingly). Space is allocated dynamically so
- the actual size of the virtual drive should not grow unless
- you use it
-
-6.0.4 -- 13 Jun 2011
-
- * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
-
-6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4]
-
- * Updated to Debian squeeze 6.0.1
- * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
- * Appliance is available as a single file (.ova) ready for the import
-
-6.0.2 -- 08 Feb 2011
-
-6.0.1 -- 01 Dec 2010
-
-Documentation
--------------
-
-The virtual machine contains an installation of `Debian 6.0 (squeeze)`_ with a
-GNOME_ desktop environment. All installed software comes from standard Debian
-packages, or prospective Debian packages from NeuroDebian. This means that all
-contained software is readily available for any system running a Debian
-operating system (or a recent Ubuntu release). The virtual machine can be seen
-as a showcase of what Debian for neuroscience research feels like. Moreover,
-once downloaded this virtual machine can be kept up to date, just as any other
+The virtual machine contains an installation of `Debian 7.0 (wheezy)`_ with a
+XFCE4_ desktop environment. All installed software comes from standard Debian
+packages, or prospective Debian packages from NeuroDebian. The virtual machine
+can be seen as a showcase of what Debian for neuroscience research feels like.
+Once downloaded this virtual machine can be kept up to date, just as any other
Debian installation. Using convenient graphical package management tools users
will benefit from security bug fixes provided by the Debian project for the
whole operating system, as well as from software updates for
neuroscience-related packages.
-.. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze
-.. _GNOME: http://www.gnome.org/
+Even on Debian-based systems this virtual machine is an excellent way to
+maintain an analysis environment that remains identical throughout the lifetime
+of a study and that can be archived alongside acquired data and publications.
+This is a much more practical way than freezing the entire software stack of a
+whole workstation, where it quickly becomes troublesome to combine the desire
+for latest research methodology for new studies and the need for stability for
+ongoing projects.
Installation
~~~~~~~~~~~~
-The following video shows how to get the NeuroDebian virtual machine running
-on your machine. The installation is shown for Mac OS X. It should, however, be
-very similar on a Windows box. If you cannot watch the video, please take a
-look at the written instructions below.
-
-.. raw:: html
+The following instructions demonstrate how to install the NeuroDebian virtual
+machine -- here shown exemplary for Mac OS X, but the procedure is virtually
+identical on a Windows box. There is also a video tutorial at coffee break
+length. `[Virtual machine setup video tutorial]
+<http://www.youtube.com/watch?v=eqfjKV5XaTE>`_.
- <iframe title="YouTube video player"
- class="youtube-player"
- type="text/html"
- width="640"
- height="375"
- src="http://www.youtube.com/embed/eqfjKV5XaTE?hd=1"
- frameborder="0"></iframe>
-
-First download and install a recent version of VirtualBox_. VirtualBox is a
-virtualization software that is freely available for Windows, MacOS X, Solaris,
-and Linux. VirtualBox comes with a comprehensive manual that should answer
-potential questions regarding installation and maintenance.
+If you don't have t already, first download and install a recent version of
+VirtualBox_. VirtualBox is a virtualization software that is freely available
+for Windows, MacOS X, Solaris, and Linux. VirtualBox comes with a comprehensive
+manual that should answer potential questions regarding installation and
+maintenance.
.. _VirtualBox: http://www.virtualbox.org
-Next, download the most recent version of the NeuroDebian virtual machine from
-the Downloads_ section. Start VirtualBox and select "Import Appliance" from the file
-menu.
+Obtain the most recent version of the NeuroDebian virtual machine by visiting
+http://neuro.debian.net and selecting your operating system and a download
+server on the frontpage.
+
+Start VirtualBox and select "Import Appliance" from the file menu.
.. image:: pics/vm_import_app.jpg
.. image:: pics/vm_settings.jpg
-The virtual machine logs yourself in automatically. The name of the virtual
-machine user is `brain` and the password is `neurodebian`. The *root* password
-is also `neurodebian`. In most cases, however, you should not be forced to type
-the password, since `sudo` is configured to work without it.
+The virtual machine logs yourself in automatically. This is the default account:
+
+:user: brain
+:password: neurodebian
+
+:root password: neurodebian
+
+In most cases you should not be forced to type the password, because ``sudo``
+is configured to work without it.
.. note::
Working with the virtual machine
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-The next video is a demonstration of some basic desktop integration features.
-It shows how to use the virtual machine in full-screen and seamless mode, shared
-folder access, software installation, as well as suspending and resuming the
-virtual machine.
-
-.. raw:: html
-
- <iframe title="YouTube video player"
- class="youtube-player"
- type="text/html"
- width="640"
- height="375"
- src="http://www.youtube.com/embed/OV7fYSEoOeQ?hd=1"
- frameborder="0"></iframe>
+The NeuroDebian virtual machine has very low maintenance demands. We have
+prepared a short video demo that shows most typical procedures that you will
+probably perform while working with NeuroDebian inside a virtual machine:
+use the virtual machine in full-screen and seamless mode, shared folder access,
+software installation, as well as suspending and resuming the
+virtual machine. `[Virtual machine handling video tutorial]
+<http://www.youtube.com/watch?v=OV7fYSEoOeQ>`_
.. _chap_vm_troubleshooting:
Troubleshooting
~~~~~~~~~~~~~~~
-Updating the VM or installing new packages doesn't work.
+.. container:: foldup
+
+ .. container:: expandinstructions
+
+ Click on an item to expand it
+
+ Updating the VM or installing new packages doesn't work
+ The VM uses as service that tries to figure out the best/closest package
+ repository for you. In some network environments this service might not work
+ well, or not at all. To check if this is a problem, you can modify the
+ respective configuration by hand. Edit ``/etc/apt/sources.list`` (you need
+ to use ``sudo`` for that) and replace the package repository URL with a
+ mirror close to you. A comprehensive list of mirrors is available at:
+ http://www.debian.org/mirror/list
+
+ Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
+ URL. For example, in Canada you might want to change::
+
+ deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
+
+ to::
+
+ deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
+
+ Only modify lines that refer to ``geomirror`` (all of them), but do **not**
+ modify entries for ``security.debian.org``.
+
+ Our proxy setup at work prevents APT from downloading packages
+ APT needs to be told how to access the proxy. Talk to your local sysadmin
+ and ask for the proxy's address (maybe a username and password too), as well
+ as the ports for HTTP and FTP proxies. With this information add the
+ following lines in the file, /etc/apt/apt.conf.d/80proxy. This will ensure
+ that after an upgrade changes won't be lost::
+
+ Acquire::http::proxy "http://<username>:<password>@<proxy>:<port>/";
+ Acquire::ftp::proxy "ftp://<username>:<password>@<proxy>:<port>/";
+ Acquire::https::proxy "https://<username>:<password>@<proxy>:<port>/";
+
+ I cannot hear sounds played in the virtual machine
+ By default the sound is muted. To enable playback launch the mixer applet by
+ clicking on the mixer icon in the task bar. Unmute the master volume
+ control. Now click on the "Volume control" to load the channel mixer dialog.
+ Unmute the "Master" and "PCM" channels and raise the volume as desired. You
+ should now be able to hear sounds played within the virtual machines through
+ your host computer's speakers.
+
+ My VM lost mounted host directories after upgrading from VirtualBox from 3.x to 4.x
+ NeuroDebian VMs prior 6.0.3 were shipped with guest additions from
+ 3.x series of VirtualBox and some initial versions of VirtualBox in
+ 4.x series have failed to mount host directories properly.
+ VirtualBox 4.0.8 seems to work fine with guest additions from 3.x
+ series. If you nevertheless want to upgrade guest additions within
+ NeuroDebian VM, please rebuild the version available from the
+ backports::
+
+ sudo apt-get install -y linux-headers-2.6-`dpkg --print-architecture`
+ sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
+ virtualbox-ose-guest-utils virtualbox-ose-guest-x11
+
+ and reboot VM.
+
+ My VM lost mounted host directories, and display auto-resizing after upgrade
+ NeuroDebian VMs ship without Linux kernel headers pre-installed to
+ minimize distribution/running footprint for one time throw-away
+ usages of the VM. To install headers package(s) just run
+
+ sudo apt-get install -y linux-headers-`dpkg --print-architecture`
+
+ and reboot VM.
+
+ I am still running an older VirtualBox 3.x
+ Download one of the image files listed below. These older releases
+ are distributed as a `zip` file. Please extract all files from the
+ `.zip` file, using appropriate software for your operating system.
+
+ * `NeuroDebian 6.0.2 image (32bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]
+
+ * `NeuroDebian 6.0.2 image (64bit)
+ <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]
+
+
+What has changed
+----------------
+
+.. container:: foldup
+
+ .. container:: expandinstructions
+
+ Click on an item to expand it
+
+ 7.8.0 -- 2 Feb 2015
+ * VM appliance based on the updated wheezy point release 7.8.0.
+ Should resolve problems with upgrades of the guest additions.
+
+ 7.4.20140423 -- 24 Apr 2014
+ * VM appliance based on the updated wheezy point release 7.4.
+ Should resolve problems with upgrades of the guest additions.
+ See http://neuro.debian.net/faq.html#comment-1351846812
+
+ 7.4.0 -- 28 Feb 2014
+ * VM appliance based on the official wheezy point release 7.4.
+
+ 7.2.0 -- 03 Nov 2013
+ * VM appliance based on the official wheezy point release 7.2.
+ * Ships with updated neurodebian-* packages:
+ - installs ipython notebook and qtconsole for "Scientific Python"
+ and "PyMVPA tutorial" welcome wizard choices.
- The VM uses as service that tries to figure out the best/closest package
- repository for you. In some network environments this service might not work
- well, or not at all. To check if this is a problem, you can modify the
- respective configuration by hand. Edit ``/etc/apt/sources.list`` (you need to
- use ``sudo`` for that) and replace the package repository URL with a mirror
- close to you. A comprehensive list of mirrors is available at:
- http://www.debian.org/mirror/list
+ 7.0.0 -- 15 May 2013
+ * VM appliance based on the official wheezy release.
+ * Uses xfce4-terminal by default (instead of urxvt/rxvt-unicode as
+ in beta-releases)
- Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
- URL. For example, in Canada you might want to change::
+ 6.999.b4.20130421 -- 22 Apr 2013
+ * Refreshed VM appliance to avoid lengthy initial upgrade
- deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
+ 6.999.b4.20121231 -- 31 Dec 2012
+ * Based on beta 4 release of debian-installer_ for wheezy
+ * Comes with XFCE4_ instead of GNOME_
- to::
+ 6.0.6 -- 01 Oct 2012
+ * Updated core system to Debian squeeze 6.0.6
- deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
+ 6.0.5 -- 10 Nov 2011
+ * Updated core system to Debian squeeze 6.0.3
+ * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.10
- Only modify lines that refer to ``geomirror`` (all of them), but do **not**
- modify entries for ``security.debian.org``.
+ - ``~/host`` is now symlinked to correct path ``/media/sf_host``
+ - ``brain`` user is added to ``vboxsf`` group so mounted host
+ directories should become readily available
-I cannot hear sounds played in the virtual machine.
+ * Root partition size and swap space got doubled in size (40GB
+ and 2GB correspondingly). Space is allocated dynamically so
+ the actual size of the virtual drive should not grow unless
+ you use it
- By default the sound is muted. To enable playback launch the mixer applet by
- clicking on the mixer icon in the task bar. Unmute the master volume control.
- Now click on the "Volume control" to load the channel mixer dialog. Unmute
- the "Master" and "PCM" channels and raise the volume as desired. You should
- now be able to hear sounds played within the virtual machines through your
- host computer's speakers.
+ 6.0.4 -- 13 Jun 2011
+ * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
-I have upgraded VirtualBox from 3.x series to 4.x, and my VM lost
-mounted host directories.
+ 6.0.3 -- 12 Jun 2011 [Superseded in the archive by 6.0.4]
+ * Updated to Squeeze 6.0.1
+ * Updated VirtualBox guest additions to 4.0.4 from backports.debian.org
+ * Appliance is available as a single file (.ova) ready for the import
- NeuroDebian VMs prior 6.0.3 were shipped with guest additions from
- 3.x series of VirtualBox and some initial versions of VirtualBox in
- 4.x series have failed to mount host directories properly.
- VirtualBox 4.0.8 seems to work fine with guest additions from 3.x
- series. If you nevertheless want to upgrade guest additions within
- NeuroDebian VM, please rebuild the version available from the
- backports::
+ 6.0.2 -- 08 Feb 2011
+ * Minor update
- sudo apt-get install -y linux-headers-2.6-amd64 # or -686 for 32bit
- sudo apt-get install -y -t squeeze-backports virtualbox-ose-guest-dkms \
- virtualbox-ose-guest-utils virtualbox-ose-guest-x11
+ 6.0.1 -- 01 Dec 2010
+ * Minor update
- and reboot VM.
+.. include:: link_names.txt
projects / neurodebian.git / blobdiff