[Neurodebian-users] running neurodebian Singularity container on Redhat EL6?

[Bennet Fauber]

Craig,

If you install the neurodebian-desktop, it adds a NeuroDebian menu to
the interface.  Those menu items will prompt you to install a package
(and provide the sudo password) if it isn't yet.  I believe the menu
items call nd-autoinstall.  You can try

$ nd-autoinstall --help

or see the man page for it.

I am not sure which will be better for your situation.  Sorry.

-- bennet


On Mon, Aug 28, 2017 at 4:33 PM, Craig Hamilton <crhamilt at gmail.com> wrote:
> I’m making progress, lots of googling for answers.  What menu are you referring to ‘at first use from the menu’?  Is there indeed a ‘software suite’, or is that just the collection of packages that I decide to install myself?  I’ll try to contact the maintainer you suggested.
>
> Thanks
>
>> On Aug 28, 2017, at 1:25 PM, Bennet Fauber <bennet at umich.edu> wrote:
>>
>> Craig,
>>
>> It might be a stock NeuroDebian, in which case the software is
>> designed to install at first use from the menu.  Probably that
>> question is best aimed at the maintainer of the Singularity Hub ND
>> container.  I don't know if that's handled on the ND mailing list or
>> on the Singularity mailing list.
>>
>> But, yes, I think you'll end up running something to actually install
>> what you want.
>>
>> Be careful about the container size, too!  I have ended up making
>> multiple containers because I didn't know how large it would be with
>> the final software suite installed.
>>
>> Good luck!  Let me know how it turns out, if you have a moment.  I'm
>> curious whether this might be good on our cluster or not.
>>
>> -- bennet
>>
>>
>>
>>
>> On Mon, Aug 28, 2017 at 1:19 PM, Craig Hamilton <crhamilt at gmail.com> wrote:
>>> Thanks for the speedy reply, Bennet!  You are right about uname.  os-release does show debian, so I think
>>> it is working.  It seems that there is no neuro software installed, I will need to apt-get lots of stuff.  I guess I
>>> didn’t understand that the neurodebian container is just a bare OS, and all the packages I want to use have
>>> to be manually installled.   I initially thought that neurodebian meant you download one big package and
>>> you get a multitude of tools at once.   Am I understanding this correctly?  (The documentation could
>>> really use some work…)
>>>
>>> Best,
>>>  Craig
>>>
>>>
>>>> On Aug 28, 2017, at 1:02 PM, Bennet Fauber <bennet at umich.edu> wrote:
>>>>
>>>> Craig,
>>>>
>>>> I think uname will return the host kernel version, not the container version.
>>>>
>>>> From the Singularity shell, try
>>>>
>>>> $ cat /etc/os-release
>>>>
>>>> You will almost certainly have to set up your paths inside the
>>>> container as part of setting up the application you want to run.
>>>> Singularity isn't a VM, it's really an application container, so
>>>> setting paths and the like would be part of the application you run,
>>>> which might be a shell script.
>>>>
>>>> So, try something like this from the container shell.
>>>>
>>>> $ export FLSDIR=/usr/share/fsl/5.0
>>>> $ source $FSLDIR/etc/fslconf/fsl.sh
>>>> $ which bet2
>>>>
>>>> and see if you get something useful.
>>>>
>>>> -- bennet
>>>>
>>>>
>>>>
>>>> On Mon, Aug 28, 2017 at 12:52 PM, Craig Hamilton <crhamilt at gmail.com> wrote:
>>>>> I have a system running Redhat EL6 and want to be able to use neurodebian on it.  One solution I tried is:
>>>>>  1. Build singularity from source
>>>>>  2. Run “singularity pull shub://neurodebian/neurodebian”  which downloads a 12GB Singularity container.
>>>>>  3. Run “singularity shell neurodebian-neurodebian-master.img”
>>>>>  4. I get a shell prompt within the container, but don’t find any neuro software available anywhere.
>>>>>      If I run ‘uname -a’ at the container shell prompt, it returns redhat linux, not debian. The file system is
>>>>>      very different than the underlying system’s file system, so I think I am inside the container.
>>>>>
>>>>> Am I wasting my time trying to do this?   Singularity seems like a great solution, but do I need to be
>>>>> running inside a debian VM?  That seems like an extra, unnecessary layer.
>>>>>
>>>>> As you can tell, I’m new to all this, any help much appreciated!
>>>>>
>>>>> Thanks,
>>>>>  Craig Hamilton
>>>>>  Wake Forest Sch of Med
>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Neurodebian-users mailing list
>>>>> Neurodebian-users at lists.alioth.debian.org
>>>>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
>>>
>