[Debian-med-packaging] environment modules for Debian Med

[Afif Elghraoui]

Hello,

On الأربعاء 16 أيلول 2015 18:06, Kevin Murray wrote:

> On 06:42 16/09, Afif Elghraoui wrote:
>>
>> +1 for environment modules. I wanted to bring this up for a long time (I
>> didn't know it's been suggested before). It might be better brought up
>> on -devel since this is something that can help Debian as a whole, in my
>> opinion.
>>
>> I may volunteer to consider its implementation. I just have several
>> packages I'm trying to create and I still need to update you all on the
>> automatic backports system.
>>
> 
> I'm in the process of setting up a ~1000 core bioinformatics cluster which will
> use environment modules quite heavily. I'd be keen for obvious reasons to see
> this happen, and am happy to lend a hand.
>

Cool! I probably will not be doing anything on this anytime soon,
though, so don't feel like you have to wait for anything.


> One initial thought: Would it be possible to hack a .deb-to-module converter?
> Or even implement something like dh_environment_modules, which works with a
> file similar to debian/<pkg>.install but auto-creates a module file adding the
> relevant paths to the environment? That would take a lot of tedious boilerplate
> away from the creation of modules, and free up sysadmin time (in my case, to
> work on Debian :]).
>

I like your debhelper extension idea.


> I particularly see this as important with packages (like samtools) with a good
> reason to have two stable versions on one system (many tools/people still rely
> on samtools < 1.0). GCC is another example of this, but probably a little out
> of scope initially.
>
> 
> We could even (and I'm not sure how Debian policy compliant this is) turn
> packages like samtools into a virtual package, requiring at least one of
> samtools-1.x or samtools-0.x, and install module files with each of the real
> packages. Just thinking out loud here :).
> 


There are two problems-- one is the one you mentioned about being able
to install different versions of the same package simultaneously (which
is important as you noted). The other is to deal with namespace
conflicts [1]. Andreas has given the plink package as an example
before-- if I understood correctly, it installs an executable with the
same name as one of the programs that PuTTY installs, so maybe every
blend metapackage can provide a module to be able to load/unload the
specified packages.


regards
Afif


1. http://blends.debian.org/blends/ch06.html#namespace

-- 
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name