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 <[email protected]> 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 <[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
