tomtoothfairies/pathways repository overview

• Tom and the Toothfairies ** Installation This project includes a Dockerfile (targeting Ubuntu 16.04) for easy installation and testing. Installation instructions for Docker on your platform can be found [[https://www.docker.com/products/docker][here⁠]].

For Docker installations on Ubuntu sudo is required to run Docker commands unless you add your user to the docker group as outlined [[http://askubuntu.com/a/477554][here⁠]]. *** The Happy Path If you do not wish to build the Docker container yourself you can run it directly from the Docker registry. First, install the necessary Docker components for your operating system as outlined above.

Then you can run the latest release from [[https://hub.docker.com/r/tomtoothfairies/pathways/][Docker⁠ Hub]] #+BEGIN_SRC bash $ docker pull tomtoothfairies/pathways:latest $ docker run tomtoothfairies/pathways #+END_SRC

To run a release other than the current you may manually specify the Docker image release tag. For example: #+BEGIN_SRC bash $ docker run tomtoothfairies/pathways:0.0 #+END_SRC

*** Building Manually There are DNS problems when running containers in Ubuntu within the TCD network. This can be resolved while on the TCD network by editing the Docker DNS config. #+BEGIN_SRC bash $ echo "{"dns": ["134.226.251.200", "134.226.251.100"]}" | sudo tee -a /etc/docker/daemon.json $ sudo service docker restart #+END_SRC You should revert these settings when leaving the TCD network by running #+BEGIN_SRC bash $ sudo rm /etc/docker/daemon.json $ sudo service docker restart #+END_SRC

1. Clone the Repo #+BEGIN_SRC bash $ git clone https://github.com/tom-and-the-toothfairies/pathways.git⁠ #+END_SRC
2. Build with Docker #+BEGIN_SRC bash $ cd pathways $ docker build -t tomtoothfairies/pathways . #+END_SRC NOTE - [[https://github.com/jnoll/peos][peos⁠]] builds on Ubuntu 16.04 but emits warnings which can be ignored.
3. Run the tests #+BEGIN_SRC bash $ docker run tomtoothfairies/pathways #+END_SRC This will run pmlcheck on a [[https://github.com/jnoll/peos/blob/master/compiler/models/martini.pml][sample⁠ pml file]], then load a subset of DINTO and report the number of triples.

** Development Docker can be used for development as follows: #+BEGIN_SRC bash $ cd pathways $ docker run -v $PWD:/code -it --rm tomtoothfairies/pathways bash #+END_SRC This will run bash in a container with the current working directory available at /code in the container