[Neurodebian-users] Trying build mriqc singularity from Docker

[Bennet Fauber]

It appears that the 3dSkullStrip binary that is included in the MRIQC
Docker image, which installs afni via ND has a reference to libGL.so.1
that is not a reference to a dynamic library in it.

$ ldd 3dSkullStrip
[ . . . output edited for brevity . . . ]
libGLw.so.1 => /usr/lib/x86_64-linux-gnu/libGLw.so.1 (0x00007f92f19e8000)
libGLU.so.1 => /usr/lib/x86_64-linux-gnu/libGLU.so.1 (0x00007f92f0482000)
libGL.so.1 (0x00007f92f0210000)

That seems, in turn, to force it to look for
/usr/lib/x86_64-linux-gnu/libGL.so, but that library is now being
installed, instead, into /usr/lib/x86_64-linux-gnu/mesa/libGL.so, and
so it is not being found.

I've been able to get this to work by using

ln -s /usr/lib/x86_64-linux-gnu/mesa/libGL.so.1.2.0 \
   /usr/lib/x86_64-linux-gnu/libGL.so.1

but I wonder whether this is indicative of a change needed in the AFNI
build so that instead of a location reference for that library, it has
a call to the loader (I think I got the jargon right)?

Thanks,  -- bennet



On Sat, Oct 7, 2017 at 1:03 PM, Bennet Fauber <bennet at umich.edu> wrote:
> I create a Singularity container using this singularity image definition file.
>
> test.def
> ==========================================
> Bootstrap: shub
> From: singularityhub/neurodebian
> ==========================================
>
> I get an image.  When I try to instal fsl-core, I get
>
>>  apt-get install fsl-core
> Reading package lists... Done
> Building dependency tree
> Reading state information... Done
> Package fsl-core is not available, but is referred to by another package.
> This may mean that the package is missing, has been obsoleted, or
> is only available from another source
>
> E: Package 'fsl-core' has no installation candidate
>
> That agrees with
>
>>  apt-cache search fsl
> . . . .
> fslview - viewer for (f)MRI and DTI data
> fslview-doc - Documentation for FSLView
> . . . .
>
> and if I
>
>> apt-get install fslview
>
> I do get a long list of packages that will install.
>
> I am really trying to resolve an issue with the mriqc Docker image
> that is missing libGLw.so.1, and I was thinking if I could build the
> ND Singularity image, I might make some headway.
>
> Which of the wrong paths have I taken?