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

[Yaroslav Halchenko]

On Thu, 19 Jul 2012, 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?

well -- between those particular two -- not that many ATM, only 

$> for f in *; do [ -e ../../afni/bin/$f ] && ls -l $f ../../afni/bin/$f; done
-rwxr-xr-x 1 root root 23656 May  3 15:51 ../../afni/bin/whirlgif*
-rwxr-xr-x 1 root root 28024 Jun 12 15:10 whirlgif*


which refer to the same tool (of different versions) which might be worth
packaging/maintaining separately anyways.  BUT such names as e.g. 'mm', 'mean',
etc are too generic, e.g. we already have 

multimail: /usr/bin/mm

with a number of such cmdline tools provided by each of such packages
probability of collisions grows up -- I bet you might find more (and
IIRC there were more in previous versions).  Ideally IMHO those
projects (or contributors) could come up with a gateway script/runner,
so any particular command then would be invoked in a way git, cmtk, etc
are doing, e.g.

fsl mm
fsl mean
fsl susan
...

which would provide convenient way to run them without any collision

> On Thursday, July 19, 2012 11:36:39 Yaroslav Halchenko wrote:
> > man fsl
> > man afni

> > provide glorious details on how to tune bashrc

> > the reason why it is not so by default is simple -- collisions among
> > cmdline utilities this toolkits provide.  That is why any fsl-VERSION
> > pkg also provides /usr/bin/fslVERSION-* symlinks

> > hope this helps

-- 
Yaroslav O. Halchenko
Postdoctoral Fellow,   Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
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