On Wed, Sep 18, 2013 at 2:24 AM, Guest, Simon
<simon.gu...@agresearch.co.nz> wrote:
> Hi Bjoern,
>
> I can see man years of effort being spent on solving this problem within
> Galaxy. I was going to title this email "Danger, Will Robinson", but I didn't
> want to be disrespectful.  I think the path being embarked upon, tool
> dependency packaging, tool versioning, reproducibility, and long term
> archive of source tarballs is going to lead inevitably to creation of a
> new Linux distribution, which I guess will be called Galaxy Linux.

It is potentially broader than that - some people are trying to cover
Mac OS X as well, and there are already Galaxy installations which
send jobs to Windows machines but that isn't something the Tool
Shed currently tackles or aims to tackle (as far as I know).

> The packaging and archival you are talking about is exactly the
> service provided by a Linux distribution.  There's well established
> infrastructure to handle this, and years of experience have gone
> into solving the problems well.  Surely the number of Linux
> distributions in the world now exceeds 100, but I don't see that
> the world will become a better place if we increase that number
> by one more.

Of course, but that isn't really what the Galaxy team want either.

> We at AgResearch can't be alone in having to pick a Linux
> distribution to run from the short list supported by our hardware
> vendor.  I can't see Galaxy Linux being on that list anytime soon.
> So we have to make Galaxy run on the particular distribution
> we have here.  For us that's CentOS 6.

We are also using CentOS, which for a while was dictated by
our IT department, but I think things are more flexible now.

Given most (non-cloud) Galaxy installations will be connected
to pre-existing clusters, rarely will the Galaxy administrators
be in a position to dictate which flavour of Linux the cluster
or grid should run.

i.e. Galaxy can't pick on Linux distribution as the only
supported platform.

> Now, I see scary mention of platform independence as a goal
> for Galaxy packaging, which I interpret as "will run on any Linux
> distribution".  I think that's essentially infeasible.  All you can
> do is write install scripts which you hope are portable (by
> following as many best practices as you know about), and
> then work patiently with users on strange platforms, to adapt
> each install script to work on that platform also.  I think this is
> not a good use of anyone's time.

In general I agree it is an open ended problem, and I have
spent more of my time than I expected on this. However,
in many cases is it quite feasible - where the authors of the
tool being wrapped for Galaxy already provide neutral Linux
binaries which should work on any recent distribution, or
use a standard configure/make system for compiling with
only 'core' header files needed.

> How many Linux distributions do the Galaxy community
> actually care about today?  The RHEL family is surely
> important, as is Ubuntu LTS.  Anything else?  I'd be quite
> interested to understand this, as it provides a context for
> the discussion, and ensures we're not just solving a
> hypothetical problem.

If you broaden that to the RHEL family (which includes
CentOS) and the Debian family (which includes Ubuntu
and Bio-Linux) then I suspect that is a majority.

> I'm just starting work on a native packaging infrastructure
> for Galaxy, that will enable tool dependencies to use defined
> versions of natively installed packages.  That frees me up
> to make my packages work nicely on the RHEL family. It
> looks like the RPMs themselves (including SRPMs obviously)
> will be hosted by the CentOS project before too long.  Once
> they're there, they can easily be archived forever.  Anyone
> else on that platform is welcome to use the same infrastructure.
> Then, all we really need is someone to handle the packaging
> effort for the other major Linux distributions (a small number,
> I hope), and the problem is essentially solved.  Getting the
> Bio-Linux team interested in multi-version packaging would
> be a great next step.

If any major Linux distributions could handle multiple versions
of tools installed in parallel via their packaging infrastructure
it would be great - at least for open source tools.

Non-open source tools would still be problematic and need
either manual install or scripting of some kind, as now.

> I'll be posting here when I have progress to report on my
> native packaging effort.
>
> cheers,
> Simon

That sounds promising,

Thank you,

Peter
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