[Neurodebian-devel] afni, fsl commands in path by default?

[Michael Hanke]

Hi,

On Thu, Jul 19, 2012 at 11:43:59AM -0400, Benjamin Kay wrote:
> I am not aware of any collisions, although that certainly doesn't mean
> they aren't a problem for some users. Could you please supply an
> example?

This is probably the most frequently discussed issue. Let me put the
conclusions first: the current situation is the best one, but it is
still broken -- Yarik already outlined how it should really be done.

The actual collision figures change over time, but for the sake of
future reference here is the current blame-list
(<package>: <file_provided>):

/usr/share/fsl/4.1/bin % for i in *; do apt-file search "/usr/bin/$i "; done
yagiuda: /usr/bin/first
im: /usr/bin/immv
im: /usr/bin/imrm
cyrus-clients-2.4: /usr/bin/imtest
multimail: /usr/bin/mm
tsung: /usr/bin/tsplot

/usr/lib/afni/bin % for i in *; do apt-file search "/usr/bin/$i "; done
joystick: /usr/bin/fftest 
im: /usr/bin/imcat 
wcstools: /usr/bin/imstack

This list only covers packages in Debian proper -- not necessarily all
software available from NeuroDebian. Putting FSL/AFNI in the default path,
will break all these packages. You might want to argue that a machine
where FSL is used would never also use any of the above packages, but
that is not guaranteed -- especially in the context of multi-user,
multi-purpose machines (think big compute clusters).

The only way forward is to fix FSL (and all the others) to use a gateway
script/binary like other big software collections do....

Hope that explains,

Michael


-- 
Michael Hanke
http://mih.voxindeserto.de