I would like to : sudo apt-get singularity

[Alain Domissy]

Is there any chance of having a Singularity deb package soon ?
or a package in the official/optional Ubuntu repositories ? 

How hard would it be ? 

Would using checkinstall be a good idea : https://help.ubuntu.com/community/CheckInstall  ?

Or would it require following the official guide : http://packaging.ubuntu.com/html/ ?

 
Thanks!

Alain

[Alain Domissy]

Actually:  sudo apt-get install singularity 

[Yaroslav Halchenko]

ok, since there is a demand:

- enable http://neuro.debian.net repository:
  - follow website
  - or if you have ubuntu >= 15.10  just apt-get install neurodebian   and follow its instructions, and then do apt-get update
- apt-get install singularity-container

I thought originally to wait until it gets accepted into debian proper -- it is in the NEW queue. but since there is a demand, I have uploaded backports of 2.1~testing0+git39-g875d469-1 for all debian/ubuntu releases to neurodebian.  Give them a shot

[Alain Domissy]

Thanks!!

I followed the instructions and was not able to find the singularity-container package 

I have ubuntu 15.04 (vivid) and my apt sources include this:

cat /etc/apt/sources.list.d/neurodebian.sources.list 

deb http://neurodeb.pirsquared.org data main contrib non-free

#deb-src http://neurodeb.pirsquared.org data main contrib non-free

deb http://neurodeb.pirsquared.org vivid main contrib non-free

#deb-src http://neurodeb.pirsquared.org vivid main contrib non-free

Also I do not see singularity-container in this list:

http://neuro.debian.net/pkglists/toc_pkgs_for_release_vivid.html#toc-pkgs-for-release-vivid

Am I missing something ? Thank you so much!

[Yaroslav Halchenko]

On Fri, 05 Aug 2016, Alain Domissy wrote:

> Thanks!!
> I followed the instructions and was not able to find the

> singularity-container packageA

> I have ubuntu 15.04 (vivid) and my apt sources include this:

> cat /etc/apt/sources.list.d/neurodebian.sources.listA

> deb http://neurodeb.pirsquared.org data main contrib non-free
> #deb-src http://neurodeb.pirsquared.org data main contrib non-free
> deb http://neurodeb.pirsquared.org vivid main contrib non-free
> #deb-src http://neurodeb.pirsquared.org vivid main contrib non-free
> Also I do not see singularity-container in this list:
> http://neuro.debian.net/pkglists/toc_pkgs_for_release_vivid.html#toc-pkgs-for-release-vivid

> Am I missing something ?A Thank you so much!

since I have just uploaded it, it didn't propagate yet to the mirrors
(e.g. pirsquared in CA). The easiest resolution is just to wait for a
day... alternative -- reconfigure to use
http://neuro.debian.net/debian repository not
http://neurodeb.pirsquared.org

--
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

[Alain Domissy]

It's working great. Very useful. Thanks!

[Yaroslav Halchenko]

FWIW -- now singularity-container 2.1.2 package is also available from a stock Debian sid (AKA unstable), and thus likely might even become a candidate for upcoming stretch release.
As a reminder - NeuroDebian provides backport builds for all other Debian/Ubuntu releases: see http://neuro.debian.net/pkgs/singularity-container.html for the summary

[Gregory M. Kurtzer]

This is fantastic news Yaroslav, thank you!

I am thinking that we should update the #install doc on the website to reflect both availability on Sid native and NeuroDebian with the link you provided for all others.

BTW, seriously fantastic work with that site!

Thanks!

On Thu, Aug 18, 2016 at 9:55 PM, Yaroslav Halchenko <yarik...@gmail.com> wrote:

FWIW -- now singularity-container 2.1.2 package is also available from a stock Debian sid (AKA unstable), and thus likely might even become a candidate for upcoming stretch release.
As a reminder - NeuroDebian provides backport builds for all other Debian/Ubuntu releases: see http://neuro.debian.net/pkgs/singularity-container.html for the summary

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--

Gregory M. Kurtzer
High Performance Computing Services (HPCS)
University of California
Lawrence Berkeley National Laboratory
One Cyclotron Road, Berkeley, CA 94720

[Yaroslav Halchenko]

On Fri, 19 Aug 2016, Gregory M. Kurtzer wrote:

> This is fantastic news Yaroslav, thank you!
> I am thinking that we should update the #install doc on the website to
> reflect both availability on Sid native and NeuroDebian with the link you
> provided for all others.
> BTW, seriously fantastic work with that site!

Kudos on the website go to Michael Hanke (CCed, the other 50% of
the core of the NeuroDebian team) -- he was the one to make website
happen with that amount of detail ;)

[Dave Love]

Yaroslav Halchenko <yarik...@gmail.com> writes:

> FWIW -- now singularity-container 2.1.2 package is also available from a
> stock Debian sid (AKA unstable), and thus likely might even become a
> candidate for upcoming stretch release.

Does the setuid code meet Debian's standards for a releasable package?
I don't think it's releasable for Fedora, and I still need to consult on
what to do about that.

For what it's worth, I recently found the useful-looking
<https://research.cs.wisc.edu/mist/presentations/XSEDE2014-SecureProgramming.pdf>
from a reference to guidelines on writing secure code to which I assume
XSEDE applications are meant to adhere. Maybe something from XSEDE
carries weight. Several general points from it are addressed in the
changes under <https://github.com/loveshack/singularity/tree/2.x>.
Others aren't, like more secure file opening, which would break test.sh.

Another thing hinted at in those guidelines: I prevented sexec building
with a non-GNU libc because it doesn't sanitize the environment, and I
couldn't see anything in musl, at least, doing the job. It may not be
an issue in practice, since I doubt such libraries are used on
multi-access systems, but better safe than sorry.