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biosimulators / Biosimulators_COPASI

COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
https://docs.biosimulators.org/Biosimulators_COPASI
MIT License
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Docker run command returning "is not a file" error on omex path #60

Open AlexPatrie opened 1 year ago

AlexPatrie commented 1 year ago

Without error, I am able to call: docker pull {copasi image str}

However, when calling: docker run {copasi image str} -i {path to omex} -o {path to output}

I am greeted with the following error: {path to omex} is not a file

I have taken care to point to a .omex file and NOT the directory of omex contents.

PROPOSAL:

Refactoring docker abilities to recursively index a desired omex path. PR to come.

AlexPatrie commented 1 year ago

After doing some deep diving, I have mapped out the general schema for the container which is created by the Dockerfile within this repo using a JSON-like object. The schema is:

{ "base_image": "python:3.9-slim-buster", "version": "0.1.35", "software": "COPASI", "software.version": "4.36.260", "about": { "summary": "Open-source software package for the simulation and analysis of biochemical networks and their dynamics.", "home": "http://copasi.org/", "documentation": "http://copasi.org/Support/User_Manual/", "license_file": "https://github.com/copasi/COPASI/blob/develop/license.txt", "license": "SPDX:Artistic-2.0", "tags": "kinetic modeling,dynamical simulation,systems biology,biochemical networks,SBML,SED-ML,COMBINE,OMEX,BioSimulators" }, "org.opencontainers.image.title": "COPASI", "org.opencontainers.image.version": "4.36.260", "org.opencontainers.image.description": "Open-source software package for the simulation and analysis of biochemical networks and their dynamics.", "org.opencontainers.image.url": "http://copasi.org/", "org.opencontainers.image.documentation": "http://copasi.org/Support/User_Manual/", "org.opencontainers.image.source": "https://github.com/biosimulators/Biosimulators_COPASI", "org.opencontainers.image.authors": "BioSimulators Team info@biosimulators.org", "org.opencontainers.image.vendor": "BioSimulators Team", "org.opencontainers.image.licenses": "Artistic-2.0", "maintainer": "BioSimulators Team info@biosimulators.org", "dependencies": [ "libfreetype6" ], "entrypoint": [ "biosimulators-copasi" ], "cmd": [], "environment": { "ALGORITHM_SUBSTITUTION_POLICY": "SIMILAR_VARIABLES", "VERBOSE": "0", "MPLBACKEND": "PDF" } }

May this serve as a mapping for Dockerfile traversal.