Also for stats report which repo and which job number use our setup

[neurodebian.git] / sphinx / vm.rst

diff --git a/sphinx/vm.rst b/sphinx/vm.rst
index 3bb4716b89f348df80ab2ebf0999b2b5c42fcee2..1701ddb68eb705741c3bd2f7bb906e06c5b38e9d 100644 (file)
--- 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
 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
 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.
 
 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
 ~~~~~~~~~~~~
 
 Installation
 ~~~~~~~~~~~~


@@ -148,85 +141,155 @@ virtual machine. `[Virtual machine handling video tutorial]
 Troubleshooting
 ~~~~~~~~~~~~~~~
 
 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::

 
 

-  <div class="expandinstructions">Click on an item to expand it</div>
+      Acquire::http::proxy "http://<username>:<password>@<proxy>:<port>/";
+      Acquire::ftp::proxy "ftp://<username>:<password>@<proxy>:<port>/";
+      Acquire::https::proxy "https://<username>:<password>@<proxy>:<port>/";

 
 

-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)
+      <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_i386.zip>`_ [~545MB]

 
 

-  and reboot VM.
+    * `NeuroDebian 6.0.2 image (64bit)
+      <http://neuro.debian.net/debian/vm/neurodebian_6.0.2_amd64.zip>`_ [~560MB]

 
 
 What has changed
 ----------------
 
 
 
 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

 
 

-  <div class="expandinstructions">Click on an item to expand it</div>
+  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