How to run (locally)

[mdehollander]

Hi,

I am looking at the kbase repositories in order to run an annotation on our local server. Where can I find instructions to deploy the kbase system, including running the rast-annotate-proteins-kmer-v1.pl command locally (without making connections to the rast servers)?

Thanks!

[scottdaniel]

Although this is over a year old, I was wondering the same thing... guess it's not a "feature" yet?

[LifeWorks]

Find this fiver years later, does KBase allow local deployment?

[scanon]

If all you wanted to do was just run RAST then it would be feasible but it isn't something we have documented. KBase isn't really directly maintain RAST any longer, we just occasionally take the latest version and update it in the platform.

[djinnome]

HI @scanon I think what @LifeWorks was asking was whether you can run KBase apps locally? Even if you can't run a narrative locally, it seems like it should be possible to run one Kbase app in a docker container, and then pipe the output of the app to the input of another Kbase app in another docker container, since the input and output data types are all interoperable.

[djinnome]

for example, is it possible to start with a set of metagenomic sequence reads and take it all the way to a community metabolic model by running each app in a separate docker container on a local cluster?

[LifeWorks]

If all you wanted to do was just run RAST then it would be feasible but it isn't something we have documented. KBase isn't really directly maintain RAST any longer, we just occasionally take the latest version and update it in the platform.

Thanks for the response. Does RAST provide stand-alone version? I can hardly find it. Literally, I spent days searching for it.

What I mean locally, is not depending on the online databases, rather I can put dbs locally on the HPC, so that I do not need to rely on the internet connection.