We are going in circles here :)

Me:
"my hope is for a way of programmatically importing and updating new tools"

You:
"This is currently possible (and very simple to do) using the Galaxy Admin UI"

I would call using the Admin UI not doing some programmatically.

You have done a brilliant job making easy to install and update tools
via the Admin UI. I am not sure the experience could be made any
easier. I have been instead trying to ask about how I might script
some of the actions you have enabled via the Admin UI.

My draconian theories about production environments aside, the second
use case - fully automating the creation of preconfigured Galaxy
instances for cloud images - that requires this functionality if I
want to use tool sheds, its not a taste thing. So I am going to
implement it - I need it, I just wanted your opinion on the best way
to go about it.

We should perhaps continue this conversation via pull request.

Thanks again,
-John

On Sat, Jun 9, 2012 at 6:01 AM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> 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.
>
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_tool_shed_repository_data_types_into_a_local_Galaxy_instance
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Getting_updates_for_tool_shed_repositories_installed_in_a_local_Galaxy_instance
>
> I'm currently writing the following new section - it should be available 
> within the next week or so.
>
> http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_3rd_party_tool_dependency_installation_and_compilation_with_installed_repositories
>
>
>
>> 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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