Preamble
--------
-Sometimes research software projects start to lag behind recent
-developments in the libraries they rely upon because necessary changes
-to the code might require
-considerable effort, and thus time. That leads to
-inability to build those tools using up-to-date versions of libraries
-available on the system due to incompatible API, and sooner or later
-because of that those tools get removed from the repository.
-
-That is what happened with fslview_ tool from FSL_ suite. Today, at
-the end of 2011, it still relies on Qt library version 3 and VTK GUI
+Sometimes research software lags behind developments in libraries it relies
+upon, because necessary changes to the code might require considerable effort,
+and thus time. That leads to difficulties building those tools using
+up-to-date library versions due API incompatibility.
+
+That is what happened with fslview_ from the FSL_ suite. Today, at
+the end of 2011, it still relies on Qt3_ and VTK GUI
support for it.
+.. _Qt3: http://doc.qt.nokia.com/3.3/
+
.. note::
Last version of Qt3, 3.3.8, was released in February 2007, with
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
+Because of its age and discontinued upstream support, `Qt3 was
orphaned`_ 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,
+Qt3 deprecation. It should be made clear that it was not removed to annoy people,
but rather because it became unfeasible to maintain its robust building
-and functioning. So nowadays fslview_ package is
-present only in the previous releases of Debian and Ubuntu which carry
-libvtk5.4-qt3 library. Those are -- Debian squeeze (stable), Ubuntu
+and functioning. So nowadays fslview_ is
+present only in those previous releases of Debian and Ubuntu which carry
+the 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 APT repository
-you are using. They
-might even work. But fresh systems installations will not have them.
+releases, chances are that you still have fslview (and required
+libraries) installed although not they are not available from the APT repository
+anymore. Therefore fresh systems installations will not have them at all.
.. _`Qt3 was orphaned`: http://lists.debian.org/debian-devel/2011/05/msg00236.html
.. _`libvtk5.4-qt3`: http://packages.debian.org/search?keywords=libvtk5.4-qt3
----------
While everyone is waiting for a new release of fslview_ compatible with Qt4
-there are possible workarounds to keep research going on
-bleeding edge Debian-based releases. The first, obvious choice for a FOSS
+there are possible workarounds to keep research going on bleeding edge
+Debian-based operating systems. 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.
+bindings, possibly after building Qt3 itself. 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 hopefully painless approach -- lightweight virtualization, or chroot_
jailing, which exists in Unix-land since 1970s.
With this exercise in **4 simple steps** we will install a
complete (minimalistic) installation of Debian stable into a separate
-directory. We will provide a convenience wrapper to
+directory -- without harming the original system installation. We will provide a convenience wrapper to
run fslview as if it was installed on the "main" system. So your
-system will stay intact while you would enrich it with additional
-installation of stable Debian. Moreover if
+system will stay intact while you would enhance it with additional
+software in a stable Debian environment. Moreover if
security or critical fixes to any components of that installation
become available, this chroot
environment, being a complete Debian installation, could be as
easily upgraded as your main system, thus guaranteeing robust performance.
Although we demonstrate this setup with fslview in mind, such approach
-is generally useful for various use cases. E.g. we have used it in
+is generally useful for various use cases. For example, 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
- root access to the system while performing this setup, although
end-users of fslview would not need root access after everything
- is setup
+ is set up
- 2 additional tools -- debootstrap_ to install Debian in a directory
and a convenience utility schroot_ to "enable" such an environment
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
- to you `Debian mirror`_
+ You might like to adjust the URL to a `Debian mirror`_ closer to you
.. _`Debian mirror`: http://www.debian.org/mirror/list
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.)
+ for more options, e.g. how to specify whole groups with ``groups=...``, etc.)
-- At this point you should be able already to invoke any command
+- At this point you should already be able 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::
chmod a+x /usr/local/bin/fslview
.. note::
- You might need, or not, to become root for above operations
- depending either you are a part of ``staff`` user group.
+ You might need to become root for the above.
Optional steps
--------------
/usr/share/fsl/data/atlases /usr/share/fsl/data/atlases none rw,bind 0 0
/usr/share/data /usr/share/data none rw,bind 0 0
+ You need to be aware of the potential consequences of this second approach:
+ Any package that installs files under /usr/share/data will modify files in
+ the same directory outside the chroot as well. If you don't want to risk
+ that don't use this method and simply install the necessary data packages
+ inside the chroot environment too, as describe before.
+
.. note::
Similarly you can bind-mount any other directory you would like
to make visible in chroot. Just be careful to not "overlap"
projects / neurodebian.git / commitdiff