--- /dev/null
+:date: 2011-12-09 16:08:00
+:tags: debian, neuroscience, software, FSL, fslview, chroot, virtualization
+
+.. _chap_schroot_fslview:
+
+"Install" fslview on recent systems
+===================================
+
+Preamble
+--------
+
+Sometimes research software projects start to lag behind recent
+developments in the libraries they rely upon because it might require
+considerable effort, and thus time, to adapt them. That leads to
+inability to build those tools using up-to-date versions of libraries
+available on the system due to the change in their API, and thus those
+tools get removed from the archive.
+
+That is the situation which happened with fslview_ tool from FSL_
+suite. At the moment it still relies on Qt library version 3 and VTK
+GUI support for it.
+
+.. note::
+
+ Last version of Qt3, 3.3.8, was released in February 2007, with
+ official support by Trolltech terminated later that year.
+
+ Qt4 was first released in 2005, and current stable series 4.7
+ released appeared in September 2010).
+
+Because of the age and discontinued upstream support, Qt3 was
+deprecated in Debian, and tools relying on it were encouraged to
+migrate to use Qt4. As a result, although Qt3 itself is still present
+in Debian (and thus Ubuntu), VTK GUI support for Qt3 (package
+`libvtk5.4-qt3`_) which fslview uses, was removed from Debian due to
+Qt3 deprecation. Once again, it was not removed just to annoy people,
+but rather because it became unfeasible to maintain robust building
+and system functioning. As the result, fslview_ package is currently
+present only in the releases of Debian and Ubuntu which carry
+libvtk5.4-qt3 library. Those are -- Debian squeeze (stable), Ubuntu
+nutty and maverick. If you upgraded your system from one of those
+releases, good chance is that you still have fslview (and required
+libraries) installed although not available from the archive. They
+might even work. But fresh systems installations will not have them.
+
+.. _`libvtk5.4-qt3`: http://packages.debian.org/search?keywords=libvtk5.4-qt3
+
+Workaround
+----------
+
+While everyone is waiting for fslview_ to become compatible with Qt4
+there are possible workarounds meanwhile to keep research going on
+bleeding edge releases. The first, obvious choice for a FOSS
+enthusiast, is to build fslview_ from source by first building VTK Qt3
+bindings. While it might be educationally valuable and exciting, we
+are afraid in the end it might be more frustrating than useful.
+
+Therefore we would like to suggest another, much more straightforward
+and painless approach -- lightweight virtualization, or chroot_
+jailing. In this exercise in **4 simple steps** we will install a
+complete (minimalistic) installation of Debian stable which has
+fslview available into a directory, and provide convenience wrapper to
+run fslview as it was installed on the "main" system. Moreover, in
+case of security or critical fixes to fslview, such chroot
+environment, while being Debian installation, would be upgradeable as
+easily as your main system, thus guaranteeing robust performance.
+
+Although demonstrated here on the example with fslview, such approach
+is generally useful for various use cases. E.g. we have used it in
+the opposite situation -- on stable Debian systems we needed to run
+some software available only from Debian unstable or testing, and
+backporting of all required dependencies was either cumbersome or just
+impossible without sacrificing stability of the system.
+
+.. _chroot: http://en.wikipedia.org/wiki/Chroot
+.. _fslview: http://www.fmrib.ox.ac.uk/fsl/fslview
+.. _FSL: http://www.fmrib.ox.ac.uk/fsl
+
+
+Prerequisites
+-------------
+
+For this exercise you would need
+
+- 3--20 minutes depending on the bandwidth to the Debian mirror and
+ efficiency in cut/paste operations
+
+- root access to the system while performing this setup, although
+ end-users of fslview would not need it to use it
+
+- tools to install Debian in a directory (called debootstrap_) and
+ convenience utility to "enable" such a chroot-ed environment (called
+ schroot_)
+
+.. _debootstrap: http://wiki.debian.org/Debootstrap
+.. _schroot: http://packages.debian.org/sid/schroot
+
+
+Procedure
+---------
+
+- Install the tools::
+
+ sudo apt-get install debootstrap schroot
+
+- Choose a location with enough space (around 400 MB) and install a
+ complete Debian squeeze installation with fslview::
+
+ sudo debootstrap --include=fslview squeeze /srv/chroots/squeeze http://ftp.us.debian.org/debian
+
+ .. note::
+ You might like to adjust URL to the archive to use some closer
+ closer to you `Debian mirror`_
+
+.. _`Debian mirror`: http://www.debian.org/mirror/list
+
+- Create schroot_ configuration file ``/etc/schroot/chroot.d/squeeze``
+ with following content::
+
+ [squeeze]
+ description=Debian squeeze (6.x stable)
+ type=directory
+ location=/srv/chroots/squeeze
+ users=YOURLOGIN
+ aliases=debian,default
+
+ Replace YOURLOGIN with a comma separated list of users who should be
+ allowed to access this chroot environment (see ``man schroot.conf``
+ for more options, e.g. how to specify the groups etc.)
+
+- At this point you should already be ready to invoke any command
+ within the chroot environment, so just create a little shell script
+ ``/usr/local/bin/fslview``, make it executable and be all set::
+
+ echo -e '#!/bin/sh\nschroot -p -c squeeze /usr/bin/fslview' > /usr/local/bin/fslview
+ chmod a+x /usr/local/bin/fslview
+
+ .. note::
+ You might need to become root for above operations, or not
+ depending either you are a part of ``staff`` user group.
+
+Optional steps
+--------------
+
+Although at this point you are all set to run fslview from the
+chroot-ed environment, we would suggest a few additional steps you
+would need to perform within the chroot-ed environment, so just enter
+it with using ``schroot -c squeeze -p``, become root (via ``su``
+command, root password should be the same as on the main system):
+
+- `Enable NeuroDebian repository <http://neuro.debian.net/#how-to-use-this-repository>`_
+
+- Enable security and functionality updates::
+
+ sed -e 's,squeeze,squeeze-updates,g' /etc/apt/sources.list > /etc/apt/sources.list.d/updates.list
+ echo 'deb http://security.debian.org/ stable/updates main' > /etc/apt/sources.list.d/security.list
+ apt-get update
+ apt-get upgrade
+
+- Read ``man schroot`` on how to enable persistent sessions so that
+ chroot initiation could be done ones during boot instead of per each
+ fslview invocation
+
+If you have any comments (typos, improvements, etc) -- feel welcome to
+leave a comment below, or just email `us@NeuroDebian`_ .
+
+.. _us@NeuroDebian: http://neuro.debian.net/#contacts
projects / neurodebian.git / commitdiff