Containerisation of ModelPolisher using Docker. - Githubissues

draeger-lab / ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.

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Containerisation of ModelPolisher using Docker. #38

Closed codekaust closed 5 years ago

codekaust commented 5 years ago

Currently, every user needs to do the following steps to be able to use ModelPolisher(considering use of postgresql):

Install the correct version of JDK(<=8), install gradle, install postgresql
Setup BiGG db on postgresql(create empty db with superuser, restore dumps in it)
Download code and build the correct JAR using gradle lightJar command
Run ModelPolisher using command line while passing an instance of postgresql db

We can containerize ModelPolisher to solve this issue. These methods may be used:

Containerization of BiGG db and postgres using ubuntu base image. We can distribute the image and ModelPolisher jar for easy usage.
Containerization of whole ModelPolisher project, user can use it then interactively.

Once the proper usage of annotatedb is figured out, we can modify containerization accordingly.