search

draeger-lab / ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
MIT License
23 stars 7 forks source link

Error when running with docker-compose #82

Closed LisbethIsolde closed 4 years ago

LisbethIsolde commented 4 years ago

When using the provided docker-compose.yml file and starting according to README line 80, the container exits with an error code: $ docker-compose run -v $MODEL_DIR:/models/ java java -jar /ModelPolisher-2.0.jar --input=$INPUT_MODEL --output=$OUPUT_MODEL --annotate-with-bigg=true --add-adb-annotations=true --output-combine=true
Starting modelpolisher_biggdb ... done Starting modelpolisher_adb ... done Error: Unable to access jarfile /ModelPolisher-2.0.jar

Your README is currently working with version 2.0, newer versions of the docker image mephenor/modelpolisher are using v2.0.1, mind updating line 80 in the README from ModelPolisher-2.0.jar to ModelPolisher-2.0.1.jar?

mephenor commented 4 years ago

Thanks for the heads up. The version number will now be automatically updated in the README when gradle is run. There was a version of this implemented in the bigg-1.6 branch, but was not merged into master as the regex was not quite right. It is currently present in a fixed version in the refactoring branch, which will be merged into master today.