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SpartaABC
A web server to simulate sequences
based on indel parameters inferred using
an approximate Bayesian computation algorithm

Research Site | Pupko Group

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SpartaABC Manual

We provide a docker version of SpartaABC. Docker is a platform that allows running and sharing programs efficiently on multiple platforms. This allows running SpartaABC on any operation system that runs Docker, including Linux, Windows, and Mac OS X. If Docker is not yet installed, please visit https://www.docker.com/ to install Docker. We will demonstrate the usage of the pipeline on Linux. The full source for SpartaABC is available on Github.

(1) Installing SpartaABC

To get the latest build of SpartaABC enter the following in your terminal (in Windows, please type it in the terminal, which you can open using the command CMD from Window’s start menu):

docker pull orenavram/sparta:spartaabc

When the command ends you should see the following message:

Status: Downloaded newer image for orenavram/sparta:spartaabc
docker.io/orenavram/sparta:spartaabc

The whole process should look very similar to this:

Next please run the following two commands:

docker image tag orenavram/sparta:spartaabc spartaabc
docker rmi orenavram/sparta:spartaabc

These commands simplify calling the SpartaABC program (in technical terms, they allow simplifying the image tag). To check that everything is properly installed, please run the following command:

docker run spartaabc --help

If everything up to this point went correctly you should see the following: