biosimulators-opencor 0.0.13

Install Python package and command-line application

1. Install the requirements for OpenCOR:

   apt-get install -y \
       curl \
       libpulse-mainloop-glib0 \
       libx11-6 \
       libxext6 \
       libxslt1.1 \
       sqlite3

2. Install OpenCOR:

   url=https://opencor.ws/downloads/snapshots/2021-05-19/OpenCOR-2021-05-19-Linux.tar.gz
   curl $url | tar -xz --directory=/opt/

3. Add OpenCOR to your system path:

   export PATH=/opt/OpenCOR-2021-05-19-Linux:$PATH

4. Install pip for this version of Python:

   curl https://bootstrap.pypa.io/get-pip.py | OpenCOR -c PythonShell

5. Use pip to install this package:

   /opt/OpenCOR-2021-05-19-Linux/python/bin/python -m pip install biosimulators-opencor

Install Docker image

docker pull ghcr.io/biosimulators/opencor

Local usage

usage: opencor [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the OpenCOR <https://opencor.ws> simulation program.

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -i ARCHIVE, --archive ARCHIVE
                        Path to OMEX file which contains one or more SED-ML-
                        encoded simulation experiments
  -o OUT_DIR, --out-dir OUT_DIR
                        Directory to save outputs
  -v, --version         show program's version number and exit

Usage through Docker container

The entrypoint to the Docker image supports the same command-line interface described above.

For example, the following command could be used to use the Docker image to execute the COMBINE/OMEX archive ./modeling-study.omex and save its outputs to ./.

docker run \
  --tty \
  --rm \
  --mount type=bind,source="$(pwd)",target=/root/in,readonly \
  --mount type=bind,source="$(pwd)",target=/root/out \
  ghcr.io/biosimulators/opencor:latest \
    -i /root/in/modeling-study.omex \
    -o /root/out