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

[Benjamin Kay]

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?

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
> 
> On Thu, 19 Jul 2012, Benjamin Kay wrote:
> 
> > I've noticed that with both afni and fsl packages (and possibly others), few executables make it into $PATH without the user having to do something. Given how easy it would be to make afni and fsl commands appear in the executable search path by default (see below), is there some benefit to the current setup that justifies the considerable confusion it has created for users?
> 
> > For afni, all that would be needed is the following additional line in debian/afni.links:
> > /etc/afni/afni.sh /etc/profile.d/afni.sh
> 
> > For fsl, one would need to create debian/fsl.conf containing the line:
> > /usr/lib/fsl/4.1
> 
> > Add one line to debian/fsl-4.1.install:
> > debian/fsl.conf etc/ld.so.conf.d/fsl.conf
> 
> > And add one line to debian/fsl-4.1.links:
> > /etc/fsl/4.1/fsl.sh /etc/profile.d/fsl.sh
> 
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> 
> 
>