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draeger-lab / ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
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Version 2.1 does not work #128

Open lcottret opened 2 months ago

lcottret commented 2 months ago

Hi,

I would like to add pathway information in the polished models. The issue #97 says that this feature is implemented in the branch 2.1. However, when I run "docker compose up" in this branch, the following error appears : 

Error response from daemon: failed to create task for container: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "--config-file": executable file not found in $PATH: unknown

OS : ubuntu 22.06 Docker version : 27.1.2

Regards, Ludo

Schmoho commented 1 month ago

Hi,

sorry for the late reply, I somehow missed this ticket. First, please be aware that the 2.1 branch is very much not stable and is not intended to be stable, as it is a development branch.

I am missing some information here: I am not certain which state of the docker-compose.yml you are referring to, there have been quite some changes on them lately. In particular, I would need to know which polisher image you were using.

I am aiming to finish the 2.1 release by October. Until then, I would advise you to use this release, or try the experimental API currently supported by the MPClient.

I am aware that the Polisher is at the moment somewhat inconvenient to use. Going forward (i.e. with the stable 2.1 release) the preferred mode of usage will be the Python HTTP Client.

lcottret commented 1 month ago

Thanks ! Don't worry, I'm going to wait for the 2.1 release and look at the MPClient.