The GA4GH API needs a reference implementation about ga4gh-schemas HOT 11 CLOSED

Another goal: it should be easy to run the implementation on various cloud providers in addition to a local machine. (in other words - it should be as portable as possible)

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+1 I agreed on the original post, comprehensive and consistent with a less-is-more approach which I like :)

+1 On the second post, which goes back to the command-line driven pipeline approach I was suggesting a while back :) Though most of these would be consolidated into scripts, the trend will most likely be on the cloud by utilizing pipelines with cached data/results, such as comparing HapMap with 1000 Genomes or having an online pipelines that keep updating a cloud storage collection of buckets as new data becomes available.

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Excellent idea! Since performance isn't a key issue and clarity, readability, etc are, can I suggest Python as the implementation language? This should also tick all the boxes for portability, and a PyPI package would make it very easy for users to install and try out.

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Sounds good to me!

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@jeromekelleher - would you like to take a stab at a skeleton project?
I feel like once we can get a rough outline of the code together it will be easy to pull in contributions to flush out all the API methods.

There is a java version of v0.1 in this repo if it helps at all!

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Sounds like fun @cassiedoll, sign me up! How about I make a start on a repo in my personal github account, which we can then move into ga4gh when it's ready for input?

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Great! I'll do ya one better and create a new repo that you can fork. ga4gh/server will be up in a sec. (we can always rename it if we want later :)

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Even better, thanks! I'll report back here once there's a working skeleton.

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+1

On 6 Aug 2014, at 20:54, cassiedoll [email protected] wrote:

Another goal: it should be easy to run the implementation on various cloud providers in addition to a local machine. (in other words - it should be as portable as possible)

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I've made a PR for the initial proposal: ga4gh/ga4gh-server#1

The original repo is at https://github.com/jeromekelleher/server if you would like to browse the code there. The README should explain what has been implemented and the approach that we've taken.

Any comments would be much appreciated!

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Marking this closed as the first commit is in.
All other reference impl discussion should now happen in that repo: https://github.com/ga4gh/server

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