Hi John,

I feel this is an important topic and that others in the community are 
undoubtedly benefitting from it, so I'm glad you started this discussion.

On Jun 9, 2012, at 12:36 AM, John Chilton wrote:

> We don't pull down from bitbucket directly to our production
> environment, we pull galaxy-dist changes into our testing repository,
> merge (that can be quite complicated, sometimes a multihour process),
> auto-deploy to a testing server, and then finally we push the tested
> changes into a bare production repo. Our sys admins then pull in
> changes from that bare production repo in our production environment.
> We also prebuild eggs in our testing environment not live on our
> production system. Given the complicated merges we need to do and the
> configuration files that need to be updated each dist update it would
> seem making those changes on a live production system would be
> problematic.
> Even if one was pulling changes directly from bitbucket into a
> production codebase, I think the dependency on bitbucket would be very
> different than on N toolsheds.

These tool migrations will only interact with a single tool shed, the main 
Galaxy tool shed.

> If our sys admin is going to update
> Galaxy and bitbucket is down, that is no problem he or she can just
> bring Galaxy back up and update later. Now lets imagine they shutdown
> our galaxy instance, updated the code base, did a database migration,
> and went to do a toolshed migration and that failed. In this case
> instead of just bringing Galaxy back up they will now need to restore
> the database from backup and pullout of the mercurial changes.

In your scenario, if everything went well except the tool shed migration, an 
option that would be less intrusive than reverting back to the previous Galaxy 
release would be to just bring up your server without the migrated tools for a 
temporary time.  When the tool shed migration process is corrected (generally, 
the only reason it would break is if the tool shed was down), you could run it 
at that time.  So the worst case scenario is that the specific migrated tools 
will be temporarily unavailable from your production Galaxy instance.

A nice feature of these migrated tool scripts is that they are very flexible in 
when they can be run, which is any time.  They also do not have to be run in 
any specific order.  So, for example, you could run tool migration script 
"0002" six months after you've run migration script "0003", "0004", etc.

These scripts do affect the Galaxy database by adding new records to certain 
tables, but if the script fails, no database corrections are necessary in order 
to prepare for running the script again.  You can just run the same script 
later, and the script will handle whatever database state exists at that time.

> Anyway all of that is a digression right, I understand that we will
> need to have the deploy-time dependencies on tool sheds and make these
> tool migration script calls part of our workflow. My lingering hope is
> for a way of programmatically importing and updating new tools that
> were never part of Galaxy (Qiime, upload_local_file, etc...) using
> tool sheds.

This is currently possible (and very simple to do) using the Galaxy Admin UI.  
See the following sections of the tool shed wiki for details.


I'm currently writing the following new section - it should be available within 
the next week or so.


> My previous e-mail was proposing or positing a mechanism
> for doing that, but I think you read it like I was trying to describe
> a way to script the migrations of the existing official Galaxy tools
> (I definitely get that you have done that).
> Thanks again for your time and detailed responses,
> -John

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