Re: ARB 6.0 released

[Elmar Pruesse <epruesse@mpi-bremen.de>]

Hi Andreas!

> Do you have a list of packages that's missing in your institute?

I'm not sure it'd be helpful. The reality at our institute is that our
base distro is rather outdated (Ubuntu 10.04, update to Debian 7 is
pending). We therefore have a lot of software in /usr/local simply
because the packages are outdated in our distro.

The second category is non FOSS software. E.g. software that came with
our instruments.

The third category are tools that were part of some research paper or
thesis. They are often not very mature and don't have an upstream that
is likely to maintain the software.

> I do not know "Environment Modules" but I agree that maintaining
> several versions in a multi user environment is a problem we do
> not have very handy solutions [...]

This is the "Environment Modules" tool I was talking about:
http://modules.sourceforge.net/

It allows managing locally installed packages by providing the command
"module" to handle modification of the users' environment. Issuing e.g.
"module add arb" would modify the PATH such that it now includes the
paths to the arb binaries. It also includes versioning ("module add
arb/6.0"), dependencies and a way to persist the loaded modules for a
user. The "packages" (modules) are defined using small TCL scripts that
define which variables have to be modified and how ("prepend-path PATH
'/usr/local/arb-6.0/bin'").

All in all it's a useful way to manage locally installed software
without creating a huge mess in /usr/local.

It might be a candidate for packaging. Although it's not really "Debian
Med".

Elmar
-- 
Dr. Elmar Pruesse

Max Planck Institute for Marine Microbiology
Microbial Genomics Group
Celsiusstrasse 1 | 28359 Bremen | Germany

Jacobs University Bremen gGmbH
School of Engineering & Science - SES
Campus Ring 1 | 28759 Bremen | Germany

Tel: +49 421 2028 984
Fax: +49 421 2028 580

http://www.arb-silva.de
http://www.microbial-genomics.de