[Neurodebian-users] ND menus

[Yaroslav Halchenko]

On Thu, 04 Feb 2016, Bennet Fauber wrote:

> I would like to update the neurodebian-desktop menu items for FSL and
> FSLView, but it seems to be a bit more involved than simply changing
> version numbers.

> The layout for the fsl program seems to have changed since FSL 4.1.
> As near as I can tell from looking at the current menu item for FSL
> 4.1, it will request the autoinstaller install the fsl-4.1 and
> fsl4.1-fsl .deb packages.

> When I manually installed 'fsl', which is labeled as a 'dummy
> package', it seems to have installed many FSL packages, some of which
> are clearly data, so I am confident that is the wrong thing to include
> there.

fsl-core probably would be the right target if you wanted a skinnier
installation.  It is also a 'dummy' one which depends on correctly
versioned fsl*-core.  Although the question would be more of "what
should a user get when he wants to run FSL" -- should it be just a core
or full deployment?    greedy me would prefer "full" one ;)

> Am I interpreting things correctly that the FSL 4.1 entry should
> changed so that it is labeled FSL 5.0 (without the minor version,
> which seems to be 5.0.9) and that it should install fsl-core, which is
> labeled 'metapackage for the latest version' and appears to be for
> 5.0.9-2, and that will install the binaries without the data?

yeap

> I ask because if that includes FSLView, which has its own menu item
> with a discrete autoinstall option, then the FSL 5 menu item should
> not install FSLView.

nah -- let it install fslview as well ;)  but for fslview leave its own
fslview package

> I am not finding a good way to list what packages a metapackage will
> actually install.  I tried

> $ apt-cache showpkg fsl-core

> but the output is a bit baffling for this neophyte, e.g.,
> 5.0.9-2~nd15.04+1 - fsl-5.0-core (0 (null)) -- which seems fine -- but
> that is followed by fsl (3 5.0.3) fsl:i386 (3 5.0.3) etc.  That seems
> to imply dependencies on older versions.  I am further confused by the
> Provides: section, which says it provides 5.0.9-2~nd15.04+1 -
> 5.0.7-4-.  Does it provide both versions 5.0.9-2 and 5.0.7-4?

I guess you see that indeed two versions are provided -- one comes from
stock ubuntu may be and  another one from neurodebian.  run 

apt-cache policy fsl-core

to see detail.  But for the sake of adjusting .desktop files shouldn't
matter

> If that is not enough bafflement for you, I am further confused
> because the FSL web site seems to be distributing FSLView 3.1

> http://fsl.fmrib.ox.ac.uk/fsl/fslview/

well -- web  is the 'web of many lies' ;)

;)  that is the point of 'modularization'.  fslview is like an
independent project within fsl, which hasn't changed for a while!  So
its package wasn't updated.  When fslview sources do get updated then
we update fslview package as well.  So it is indeed of 4.0.1 version

> but the FSL web site seems to be in transition, as the link to Build
> from sources on that page leads to a page that does not yet exist.
> When I installed the fsl binary distribution for CentOS6-64, it seems
> to have come with an FSLView 3.1 binary.  The FSLView, program that
> comes with ND lists itself as 4.0.1.  (Is the source code newer and
> the FSL binary distribution out of date?)

more like their fslview  page is out of date. I believe recent fsl still
comes with that fslview 4.0.1

> If there is some obvious documentation that I should know about for
> how the Debian FSL packages are made that I should go read, please let
> me know.

sources sources!

http://git.debian.org/?p=pkg-exppsy/fsl.git
debian/ directory has all the sources and there is README.Debian-source
which explains some gory details.

> Sorry, Yaroslav.  I did warn you.

;)  just don't dig too deep.  adjust the way you see the best fit, send
PR and if I see that something needs tuning I will comment on.

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik