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

[Yaroslav Halchenko]

On Mon, 28 Aug 2017, Craig Hamilton wrote:

> Thanks, Yaroslav.  I don’t have overlays enabled, so didn’t get got by that gotcha.   Another user (Bennet Fauber) explained that uname returns info on the host kernel.  /etc/os-release shows that I am indeed in a Debian container, so that is good.  It seems there are no neuro packages installed by default, I need to be doing a lot of apt-get.  I found that my /etc/apt/sources.list needed updating for apt-get to be able to find packages.  There could certainly be better instructions on getting this up and running!

there is a number (but not all) of neuro packages installed in that
image, e.g. AFNI, FSL, hcp workbench, etc.  Any particular one which you
found missing --  compile a list?

If you need to install more, you would need to run singularity as
root (e.g. via sudo) and with -w to allow modifications within that
image.

not sure what you mean that /etc/apt/sources.list needs updating... here
is how things look for me while running that singularity container on
Centos OS 6.9


[yhalchen at discovery yoh]$ ./neurodebian-neurodebian-master.img 
Welcome to the NeuroDebian v 2.2 (Debian stretch) environment
Please source /etc/fsl/fsl.sh if you need FSL, /etc/afni/afni.sh if you need AFNI

yhalchen at discovery:~$ cat /etc/apt/sources.list
deb http://http.debian.net/debian stretch main contrib non-free

yhalchen at discovery:~$ cat /etc/apt/sources.list.d/neurodebian.sources.list 

# NeuroDebian software repository
deb     http://neuro.debian.net/debian stretch main contrib non-free
#deb-src http://neuro.debian.net/debian stretch main contrib non-free

# NeuroDebian data repository
deb     http://neuro.debian.net/debian data main contrib non-free
#deb-src http://neuro.debian.net/debian data main contrib non-free



if something doesn't work -- cut paste output 

hope this helps

-- 
Yaroslav O. Halchenko
Center for Open Neuroscience     http://centerforopenneuroscience.org
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik        
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