On Thu, Aug 29, 2013 at 3:36 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> There is a similar but probably larger set of Debian packages
> available via Debian-Med and Bio-Linux too. The catch here
> is can you install arbitrary versions of a tool in parallel? And
> I think the answer sadly is no.

This is the crucial concern for us. The standard OS packaging
approaches (RPM and DEB) do not support this except very poorly. This
is something we absolutely need. There are other package managers that
do a better job (I'm quite fond of Homebrew on OS X, NIX also looks
nice) but would add more dependencies.

> The idea of standard recipe templates (e.g. typical Python
> install) James outlined here might help:
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-August/016273.html

I (as always) think a lot can be solved through abstraction. I'm
envisioning a very high level description of what it takes to install
a package, and then have different adapters to take that and install
it for a given OS.

James Taylor, Associate Professor, Biology/CS, Emory University
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