should we have a qiime-dependencies.conf?

[qiime]

should we have a qiime-dependencies.conf?

[pdmars]

Hmm. So what happens if you just remove QIIME from the qiime-deploy config file, run qiime-deploy and use its activate.sh and then setup just qiime manually in your own directory?

[gregcaporaso]

I haven't tried, but I'm guessing it is that simple. It might be convenient to provide that file regardless though, just to facilitate this for others. I'll try it out.

[jairideout]

It'll work if you remove the QIIME target from the conf file. I don't think it's a good idea to duplicate the QIIME conf file because that places more of a burden on us when dependencies change, QIIME versions change, etc..

[pdmars]

@jrrideout I agree about maintaining duplicate QIIME conf files. @gregcaporaso Do you mostly see this as a one-off where developers who know what they're doing want to do this (so it's fine to just remove qiime from the conf file at deployment time)? Or are you wondering about long-term and an easy solution for anyone?

[jairideout]

I forgot to mention that this is how I'm using qiime-deploy on my laptop (since I have several versions of QIIME installed and want to share dependencies) and it works out pretty well.

[gregcaporaso]

I could see this as something that developers/sys admins would be doing. I guess just documenting the change that would need to be made could be a good way to go here.

[wasade]

What about relying on modules (http://modules.sourceforge.net/) for installed dependencies? This allows you to have as many different versions of whatever on the system, and the individual user just needs to use module load xxx. The loads could be scripted out very easily.

[pdmars]

@wasade That's an interesting idea. I think originally I saw qiime-deploy being more user-focused so I wouldn't have recommended relying on modules, but for cluster deployments that could be helpful. (And even if modules isn't on a system or VM image, qiime-deploy could just deploy the whole stack like it currently does.) On a somewhat related note, I've also mentioned to @dmdu the possibility of updating qiime-deploy to integrate better with chef or puppet, etc. Modules should probably also be part of that discussion.

[wasade]

+1 re: puppet. One of our admins here has a substantial amount of
experience with puppet and would likely be interested in helping

On Wed, May 8, 2013 at 2:25 PM, Paul [email protected] wrote:

@wasade https://github.com/wasade That's an interesting idea. I think
originally I saw qiime-deploy being more user-focused so I wouldn't have
recommended relying on modules, but for cluster deployments that could be
helpful. (And even if modules isn't on a system or VM image, qiime-deploy
could just deploy the whole stack like it currently does.) On a somewhat
related note, I've also mentioned to @dmdu https://github.com/dmdu the
possibility of updating qiime-deploy to integrate better with chef or
puppet, etc. Modules should probably also be part of that discussion.

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[jairideout]

Closing this as qiime-deploy now only installs non-Python dependencies.