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Dockerfile

In order to allow users to run this tools in an easy way we provide a Dockerfile that allows you to run this tool in any host with docker installed.

Prerequisits

  • Linux Machine
  • Docker service installed
  • git installed

Running ABC with docker

  1. Clone Repo: first you need to clone this repo.
git clone https://github.com/Hickerlab/msBayes.git
  1. Build Docker Image: for build docker image you need to get into repo directory, then run the following command.
docker build -t msbayes:latest .
  1. Run the first step of the procedure (for the example in the example folder it can't be run due missing .im files)

Before running this steps you need get into examples directory

docker run --rm -v /path/to/myworkspace:/workspace --name msbayes msbayes:latest convertIM.pl infile.list

/path/to/myworkspace: Path to your working directory where your have your files for work with msbayes (in this case exaples directory)

infile.list: Text plane list of your *.im files relative to your working directory

  1. Run second step.
docker run --rm -v /path/to/myworkspace:/workspace --name msbayes msbayes:latest obsSumStats.pl -T obsSS.table batch.masterIn.fromIM > obsSS.txt
  1. Run step three
docker run --rm -v /path/to/myworkspace:/workspace --name msbayes msbayes:latest msbayes.pl -c batch.masterIn.fromIM -s 7 -r 5000 -o priorfile
  1. Run step four
docker run --rm -v /path/to/myworkspace:/workspace --name msbayes msbayes:latest acceptRej.pl -p outfig.pdf obsSS.txt priorfile > modeEstimatesOut.txt
  1. Enjoy the results :)