Re: [Gmod-tripal] Precompiled chado databases

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Re: [Gmod-tripal] Precompiled chado databases

Scott Cain
(The schema list got trimmed off the list; I added it back)

Eric,

Thanks much!

Scott

Sent from Mailbox for iPad


On Wed, Feb 5, 2014 at 11:47 AM, Eric Rasche <[hidden email]> wrote:


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Hi Scott (And Siddhartha),

I've added a wiki page here: http://gmod.org/wiki/Precompiled_Chado_Databases I'm looking for a good place to link to it from elsewhere in the wiki now.

I'm a sysadmin at heart...there's very little I wouldn't like to automate. Someday I'll cleanup the code (i.e., removing my database password), and release that in case anyone else wants to run the same jobs in private instances.

I would absolutely love to see a Tripal process that did that. I know very little about tripal past the very basic usage I'd made of it a while back. If memory serves, they have some specific schema they add, I'd be happy to add custom builds with tripal schemas automatically added, if that's of interest to the tripal community.

Cheers,
Eric


On 02/05/2014 11:07 AM, Scott Cain wrote:
> Hi Eric,
>
> I agree with siddhartha: making a wiki page for this would be great. Thanks so much for making an automated tool that does this!  I think plenty of people could make use of this (for example, imagine a Tripal process that just grabbed the pre built database and loaded it!)
>
> Scott
>
>
> Sent from my iPhone
>
>> On Feb 5, 2014, at 10:58 AM, Siddhartha Basu [hidden email] wrote:
>>
>> Hi Eric,
>> Interesting project. Could you add a wiki page for this project in
>> gmod.org, might be something look into it in the future.
>>
>> thanks,
>> -sidd
>>
>>> On Wed, 05 Feb 2014, Eric Rasche wrote:
>>>
> Chado server admins,
>
> I'm not aware of how many of you regularly have to configure and deploy
> chado databases, however over time I've found that a significant portion
> of my time was spent waiting on ontologies to load.
>
> To this end (and in support of some other projects), I set up a jenkins
> job to
>
> - clone chado from SVN
> - build
> - load ontologies
> - dump database as sql
> - upload to a publicly accessible webserver
>
> This is done on a weekly basis. I'm making the compiled databases with all
> 5 ontologies loaded available to the community. They're trivial to use if
> you're just trying to install chado, as all you need to do is change the
> username in the precompiled schema
>
> sed -i "s/schema_builder/user_name/g" csb.sql
>
> and load it into the database of your choice.
>
> psql -U {user_name} -d {desintation_db} -f csb.sql
>
> This process takes ~10 seconds, compared to the 1.3 hours (according to my
> jenkins job) for regular ontology loading.
>
> Hope someone else finds this helpful! Please find the precompiled schema
> below:
>
> https://cpt.tamu.edu/~docs/chado/
>
> Installed ontologies:
>
> [1] Relationship Ontology
> [2] Sequence Ontology
> [3] Gene Ontology
> [4] Chado Feature Properties
> [5] Plant Ontology
>
> If anyone is interested in this, and would like:
>
> - other builds with different (sub)sets of ontologies
> - archived copies of schemas over time
>
> please feel free to request them and we'll add them to the jenkins
> job/make them available.
>
> NB: The caveats of this method are, of course, that none of the scripts
> are installed, and the gmod conf files are not created in GMOD_ROOT.
> However, for remote access (e.g., via Artemis), and tools that do not make
> use of GMOD_ROOT locally, this seems to be fine.
>
> Cheers,
> Eric
>
>>
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- --
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048 <tel:4046922048>
[hidden email] [hidden email]
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