.. _chap_schroot_fslview:
-"Install" fslview on recent systems
-===================================
+Chroot workaround for fslview (HOWTO)
+=====================================
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
+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 the change in their API, and thus those
-tools get removed from the archive.
+available on the system due to incompatible API, and sooner or later
+because of that those tools get removed from the repository.
-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.
+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
+support for it.
.. note::
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).
+ 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
+Because of the 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,
-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
+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
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
+libraries) installed although not available from the APT repository
+you are using. They
might even work. But fresh systems installations will not have them.
+.. _`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
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
+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
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
+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
+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
+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
the opposite situation -- on stable Debian systems we needed to run
some software available only from Debian unstable or testing, 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
+ end-users of fslview would not need root access after everything
+ is setup
-- tools to install Debian in a directory (called debootstrap_) and
- convenience utility to "enable" such a chroot-ed environment (called
- schroot_)
+- 2 additional tools -- debootstrap_ to install Debian in a directory
+ and a convenience utility schroot_ to "enable" such an environment
.. _debootstrap: http://wiki.debian.org/Debootstrap
.. _schroot: http://packages.debian.org/sid/schroot
sudo apt-get install debootstrap schroot
-- Choose a location with enough space (around 400 MB) and install a
- complete Debian squeeze installation with fslview::
+- Choose a location with enough space (600 MB should be enough) 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`_
+ to you `Debian mirror`_
.. _`Debian mirror`: http://www.debian.org/mirror/list
- Create schroot_ configuration file ``/etc/schroot/chroot.d/squeeze``
- with following content::
+ with the following content::
[squeeze]
description=Debian squeeze (6.x stable)
type=directory
- location=/srv/chroots/squeeze
+ directory=/srv/chroots/squeeze
users=YOURLOGIN
aliases=debian,default
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
+- At this point you should be able already 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
+ 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
+ You might need, or not, to become root for above operations
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):
+Although at this point you can run fslview from the chroot-ed
+environment, we would suggest a few additional steps. For some of
+them (marked with **chroot-root**) you would need to become root in a
+chroot environment via following steps:
-- `Enable NeuroDebian repository <http://neuro.debian.net/#how-to-use-this-repository>`_
+- enter chroot using ``schroot -c squeeze -p``
-- Enable security and functionality updates::
+- become root (via ``su`` command, root password should be the same as
+ on the main system)
- 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
+So here are recommended optional additions:
-- 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
+- **chroot-root**: `Enable NeuroDebian repository
+ <http://neuro.debian.net/#how-to-use-this-repository>`_. Choose
+ ``squeeze`` release and mirror of preference (remove ``sudo`` from
+ provided cmdline).
+
+- **chroot-root**: 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
+
+- Make fsl atlases accessible within the chroot environment. There
+ are two ways and you must choose only **one** of them, otherwise
+ you might damage your "main" system installation.
+
+ - **chroot-root**: Install atlases packages in the chroot-ed environment::
+
+ apt-get install fsl-atlases
+
+ Although this is the best/correct way it would require additional 200MB of
+ space, possibly duplicating what you already have installed in the
+ main system. Also it requires `enabling of NeuroDebian repository
+ in chroot environment
+ <http://neuro.debian.net/#how-to-use-this-repository>`_.
+
+ - Alternatively you can bind-mount those directories with atlases installed on the "main"
+ system within chroot. For that edit (as root on the "main"
+ system) ``/etc/schroot/default/fstab`` and add following entries::
+
+ /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
+
+ .. note::
+ Similarly you can bind-mount any other directory you would like
+ to make visible in chroot. Just be careful to not "overlap"
+ with system directories in chroot which already carry something.
+
+Also you might like to 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`_ .
projects / neurodebian.git / blobdiff