--- /dev/null
+[mirrors]
+au = http://mirror.aarnet.edu.au/pub/neurodebian
++de-m = http://neurodebian.g-node.org
+de-md = http://apsy.gse.uni-magdeburg.de/debian
+de-v = http://nd.zetatech.org
+gr = http://neurobot.bio.auth.gr/neurodebian
+jp = http://neuroimaging.sakura.ne.jp/neurodebian
+ua = http://www.neuro.webdisk.com.ua
+us-ca = http://neurodeb.pirsquared.org
+us-nh = http://neuro.debian.net/debian
+us-tn = http://masi.vuse.vanderbilt.edu/neurodebian
+
+[mirror names]
+au = Australia (AARNET)
++de-m = Germany (Ludwig-Maximilians-Universität, München)
+de-md = Germany (University of Magdeburg)
+de-v = Germany (Nikolaus Valentin Haenel, Vogtland)
+gr = Greece (Aristotle University of Thessaloniki)
+jp = Japan (Kiyotaka Nemoto)
+ua = Ukraine (Iaroslav Iurchenko)
+us-ca = USA-CA (Paul Ivanov, California)
+us-nh = USA-NH (Dartmouth College)
+us-tn = USA-TN (Vanderbilt)
+
+[release files]
+# Release files of all repositories to be contained in the website
+# Package info files for all these releases will be downloaded.
+data = http://neuro.debian.net/debian/dists/data/Release
+hardy = http://neuro.debian.net/debian/dists/hardy/Release
+karmic = http://neuro.debian.net/debian/dists/karmic/Release
+lucid = http://neuro.debian.net/debian/dists/lucid/Release
+maverick = http://neuro.debian.net/debian/dists/maverick/Release
+natty = http://neuro.debian.net/debian/dists/natty/Release
+oneiric = http://neuro.debian.net/debian/dists/oneiric/Release
+precise = http://neuro.debian.net/debian/dists/precise/Release
+squeeze = http://neuro.debian.net/debian/dists/squeeze/Release
+wheezy = http://neuro.debian.net/debian/dists/wheezy/Release
+sid = http://neuro.debian.net/debian/dists/sid/Release
+
+[release names]
+# each item here will result in the respective release being advertised
+# on the website, i.e. sources.list being available and config form contains
+# a corresponding item -- please prune an entry when a release is no longer
+# supported
+# the 'data' entry should not be changed, as this exact setting also serves as
+# a test condition in the DDE code
+data = Datasets (data)
+#etch = Debian GNU/Linux 4.0 (etch)
+lenny = Debian GNU/Linux 5.0 (lenny)
+squeeze = Debian GNU/Linux 6.0 (squeeze)
+wheezy = Debian testing (wheezy)
+sid = Debian unstable (sid)
+# EOL: May 12 2011 (Desktop) April 2013 (Server)
+hardy = Ubuntu 08.04 LTS "Hardy Heron" (hardy)
+# EOL: Oct 23 2010
+#jaunty = Ubuntu 09.04 "Jaunty Jackalope" (jaunty)
+# EOL: April 2011
+karmic = Ubuntu 09.10 "Karmic Koala" (karmic)
+# EOL: April 2013 (Desktop) April 2015 (Server)
+lucid = Ubuntu 10.04 LTS "Lucid Lynx" (lucid)
+# EOL: April 2012
+maverick = Ubuntu 10.10 "Maverick Meerkat" (maverick)
+# EOL: October 2012
+natty = Ubuntu 11.04 "Natty Narwhal" (natty)
+# EOL: April 2013
+oneiric = Ubuntu 11.10 "Oneiric Ocelot" (oneiric)
+# EOL: April 2017 (LTS)
+precise = Ubuntu 12.04 LTS "Precise Pangolin" (precise)
+
+[metadata]
+# base url: <url>/<src_pkg-name>/<file>
+source extracts baseurl = http://neuro.debian.net/debian/extracts
+# files to query
+source extracts filenames = upstream README.Debian copyright
--- /dev/null
+.. _support:
+
+Contacts
+========
+
+`Email us directly <team@neuro.debian.net>`_ with any "private"
+communication. Otherwise please use our public mailing lists, which
+exist not only to provide user-support but also to establish
+communication channels within the NeuroDebian community
+
+.. _chap_mailinglists:
+
+* neurodebian-users_: Discussions and support of NeuroDebian users
+
+* neurodebian-upstream_: General discussions and knowledge sharing
+ among developers of neuroscience software. We also use it
+ to update you with summaries of recent relevant developments in
+ Debian project
+
+* neurodebian-devel_: Technical mailing list for discussions on
+ NeuroDebian development
+
+You are welcome also to join #neurodebian IRC room on OFTC network if
+you have quick questions or want to join a live discussion.
+
+.. _chap_team:
+
+The team
+========
+
+`Michael Hanke <http://mih.voxindeserto.de>`_ and `Yaroslav Halchenko
+<http://www.onerussian.com>`_ originally started NeuroDebian (formerly the
+`Experimental Psychology Debian packaging project
+<http://alioth.debian.org/projects/pkg-exppsy>`_) and are the current project
+leaders. However, the whole project would not be possible without the work of
+over 3,000 Debian_ developers and contributors who are as enthusiastically
+building the Debian operating system.
+A number of packages that are available from the NeuroDebian repository have
+been contributed by various individuals and other teams in Debian, such as
+`Debian Med`_ and `Debian Science`_. We want to express our gratitude to all
+maintainers_ that help to make Debian_ the ultimate software platform for
+neuroscience.
+
+.. _maintainers: pkgs.html#by-maintainer
+
+
+Acknowledgements
+================
+
+We are grateful to `Jim Haxby`_ for his continued support and :ref:`endless supply of
+Italian espresso <coffeeart>`.
+
+.. _Jim Haxby: http://haxbylab.dartmouth.edu/ppl/jim.html
+
+Thanks to the following institutions and individuals for hosting a mirror:
+
+* `Department of Psychological and Brain Sciences at Dartmouth College`_
+ *[us-nh]* (primary mirror)
+* `Department of Experimental Psychology at the University of Magdeburg`_
+ *[de-md]*
+* `Neurobot at Aristotle University of Thessaloniki, Greece`_ *[gr]*
+* `Paul Ivanov`_ *[us-ca]*
+* `Medical-image Analysis and Statistical Interpretation lab at Vanderbilt`_
+ *[us-tn]*
+* `Australia's research and education network (AARNET)
+ <http://www.aarnet.edu.au>`_ *[au]*
+* Kiyotaka Nemoto (AKA Mr. Lin4Neuro_) *[jp]*
+* Iaroslav Iurchenko *[ua]*
+* `Nikolaus Valentin Haenel`_ *[de-v]*
++* `INCF G-Node at Ludwig-Maximilians-Universität München <http://www.g-node.org>`_ *[de-m]*
+
+If your are interested in mirroring the repository, please see the :ref:`faq`.
+
+.. _Department of Psychological and Brain Sciences at Dartmouth College: http://www.dartmouth.edu/~psych
+.. _Department of Experimental Psychology at the University of Magdeburg: http://apsy.gse.uni-magdeburg.de
+.. _Neurobot at Aristotle University of Thessaloniki, Greece: http://neurobot.bio.auth.gr
+.. _Paul Ivanov: http://www.pirsquared.org
+.. _Medical-image Analysis and Statistical Interpretation lab at Vanderbilt: https://masi.vuse.vanderbilt.edu
+.. _Nikolaus Valentin Haenel: http://haenel.co
+
+.. _chap_popularity:
+
+Popularity
+==========
+
+.. raw:: html
+
+ <p><img border="0" src="_files/nd_subscriptionstats.png" title="Statistics of new repository subscriptions for all supported releases. Note: subscription is only done once per machine." /></p>
+
+Popularity Contest
+------------------
+
+We encourage you to participate in the `popularity
+contest <http://popcon.debian.org>`_ (popcon), which anonymously
+collects the list of packages you installed/use on your system.
+Collecting such statistics is of particular importance for research
+software projects as a prove of an existing user-base. If upon
+installation of the system you rejected the invitation to participate
+you can always change your decision by running::
+
+ sudo dpkg-reconfigure popularity-contest
+
+.. note::
+
+ If you are deploying multiple systems through cloning, to not have
+ all systems considered as one, it would be necessary to re-generate
+ the random MY_HOSTID. Following commands ran as root should do it
+ (as root) without any interactive dialog::
+
+ sed -i -e 's,PARTICIPATE *= *.no.,PARTICIPATE="yes",g' -e '/^ *MY_HOSTID/d' /etc/popularity-contest.conf
+ DEBIAN_FRONTEND=noninteractive dpkg-reconfigure popularity-contest
+
+In addition to popcon pages for your "core" distribution (e.g. `Debian
+<http://popcon.debian.org/>`__ or `Ubuntu
+<http://popcon.ubuntu.com/>`__) you can see/get statistics for
+submissions to `NeuroDebian <http://neuro.debian.net/popcon/>`__ and
+know that you are already contributing back to the community.
+
+
: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
----------
-
-Stable (6.x series)
-~~~~~~~~~~~~~~~~~~~
-
-Based on current stable `Debian 6.0 (squeeze)`_ release. This VM
-provides a stable, well tested environment with the most of the recent
-releases available from NeuroDebian.
-
-* `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.*
-
-Development (to be 7.x series)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
-Based on upcoming `Debian 7.0 (wheezy)`_ release. Although already
-quite stable, there might be outstanding issues. This VM also
-switches from GNOME_ (v.2) desktop environment to XFCE4_. We
-recommend this VM over a stable one for anyone needing recent releases
-of tools not available for the stable VM (e.g. recent pandas) --
-**getting a complete "Scientific Python" stack with 100s of other
-Python modules was never easier**. Moreover your feedback might also
-be valuable to polish upcoming Debian wheezy release and NeuroDebian
-VM 7.0.
-
-* `NeuroDebian 6.999.b4.20121231 image (32bit)
- <http://neuro.debian.net/debian/vm/NeuroDebian_6.999.b4.20121231_i386.ova>`_ [~656MB]
-
-* `NeuroDebian 6.999.b4.20121231 image (64bit)
- <http://neuro.debian.net/debian/vm/NeuroDebian_6.999.b4.20121231_amd64.ova>`_ [~660MB]
-
-
-Historical
-~~~~~~~~~~
-
-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
--------
-
-6.999.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
-
-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
+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
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-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
+
+ and reboot VM.
+
+
+What has changed
+----------------
+
+.. container:: foldup
- 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
+ .. container:: expandinstructions
- Pick one and replace all ``geomirror.debian.net`` URLs with the new mirror
- URL. For example, in Canada you might want to change::
+ Click on an item to expand it
- deb http://i386-geomirror.debian.net/debian squeeze main non-free contrib
++ 6.999.b4.20121231 -- 31 Dec 2012
+
- to::
++ * Based on beta 4 release of debian-installer_ for wheezy
++ * Comes with XFCE4_ instead of GNOME_
+
- deb http://ftp.ca.debian.org/debian/ squeeze main non-free contrib
+ 6.0.6 -- 01 Oct 2012
+ * Updated core system to Debian squeeze 6.0.6
- Only modify lines that refer to ``geomirror`` (all of them), but do **not**
- modify entries for ``security.debian.org``.
+ 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
-I cannot hear sounds played in the virtual machine.
+ - ``~/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
- 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.
+ * 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
-I have upgraded VirtualBox from 3.x series to 4.x, and my VM lost
-mounted host directories.
+ 6.0.4 -- 13 Jun 2011
+ * Updated shipped virtualbox-ose guest-utils and guest-x11 to 4.0.4
- 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::
+ 6.0.3 -- 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
- 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
+ 6.0.2 -- 08 Feb 2011
+ * Minor update
- and reboot VM.
+ 6.0.1 -- 01 Dec 2010
+ * Minor update
+
+ .. include:: link_names.txt
projects / neurodebian.git / commitdiff