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

[Benjamin Kay]

Indeed, that should ideally be fixed upstream. Unfortunately, adding to the path in bashrc doesn't solve the problem so much as defer it (and confuse many a user, judging by the neurodebian and fsl mailing lists). Maybe we could create a system-wide script in /etc/profile.d that checks if the UID is > 1000 before setting things up? That would avoid breakage of system scripts, which are more likely to expect mm to send mail.

On Thursday, July 19, 2012 12:36:11 Yaroslav Halchenko wrote:
> 
> 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
> 
>