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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 >>>> [email protected] >>>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users >> _______________________________________________ Neurodebian-users mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/neurodebian-users
