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