X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sphinx%2Fvm.rst;h=1701ddb68eb705741c3bd2f7bb906e06c5b38e9d;hb=HEAD;hp=3bb4716b89f348df80ab2ebf0999b2b5c42fcee2;hpb=dcb046162ac6009c0643c2a8d6e7b9cd42e010db;p=neurodebian.git diff --git a/sphinx/vm.rst b/sphinx/vm.rst index 3bb4716..1701ddb 100644 --- a/sphinx/vm.rst +++ b/sphinx/vm.rst @@ -16,13 +16,9 @@ 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 -The virtual machine contains an installation of `Debian 6.0 (squeeze)`_ with a -GNOME_ desktop environment. All installed software comes from standard Debian +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 @@ -39,9 +35,6 @@ 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. -.. _Debian 6.0 (squeeze): http://www.debian.org/releases/squeeze -.. _GNOME: http://www.gnome.org/ - Installation ~~~~~~~~~~~~ @@ -148,85 +141,155 @@ virtual machine. `[Virtual machine handling video tutorial] Troubleshooting ~~~~~~~~~~~~~~~ -.. raw:: html +.. 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:: -
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+ Acquire::http::proxy "http://:@:/"; + Acquire::ftp::proxy "ftp://:@:/"; + Acquire::https::proxy "https://:@:/"; -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 + 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. - Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror - URL. For example, in Canada you might want to change:: + 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:: - deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib + 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 - to:: + and reboot VM. - deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib + 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 - Only modify lines that refer to ``geomirror`` (all of them), but do **not** - modify entries for ``security.debian.org``. + sudo apt-get install -y linux-headers-`dpkg --print-architecture` -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. + and reboot VM. -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:: + 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. - 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 + * `NeuroDebian 6.0.2 image (32bit) + `_ [~545MB] - and reboot VM. + * `NeuroDebian 6.0.2 image (64bit) + `_ [~560MB] What has changed ---------------- -.. raw:: html +.. 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. + + 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) + + 6.999.b4.20130421 -- 22 Apr 2013 + * Refreshed VM appliance to avoid lengthy initial upgrade + + 6.999.b4.20121231 -- 31 Dec 2012 + * Based on beta 4 release of debian-installer_ for wheezy + * Comes with XFCE4_ instead of GNOME_ + + 6.0.6 -- 01 Oct 2012 + * Updated core system to Debian squeeze 6.0.6 -
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+ 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 -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 - - ``~/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 - * 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 -6.0.4 -- 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 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 -6.0.3 -- 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 + 6.0.2 -- 08 Feb 2011 + * Minor update -6.0.2 -- 08 Feb 2011 - * Minor update + 6.0.1 -- 01 Dec 2010 + * Minor update -6.0.1 -- 01 Dec 2010 - * Minor update +.. include:: link_names.txt