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pha4ge / hAMRonization

Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure
GNU Lesser General Public License v3.0
138 stars 27 forks source link

Wrong Docker link #53

Closed iaconogi closed 3 years ago

iaconogi commented 3 years ago

Dear Finley, I am Giovanni Iacono from EFSA, we had a video call the other day. The compilation of the Dockerfile from https://github.com/pha4ge/hAMRonization_workflow fails at task 18 RUN cd data/test && bash get_test_data.sh && cd ../..

The reason is that in the current repository https://github.com/pha4ge/hamronization the data folder is not present. This folder is present in https://github.com/pha4ge/hAMRonization_workflow.

Also a question, the Dockerfile in https://github.com/pha4ge/hAMRonization_workflow installs only the parsers, correct ?

fmaguire commented 3 years ago

To install just the parsers in this repo you can now just run docker pull finlaymaguire/hamronization:latest and it will just install a minimal container with the python3.9 base image and hamronize as the entrypoint.

Let me know if you have any issues with the container.

iaconogi commented 3 years ago

Yes I already did a minimal container with pyhton and pip install hamronization and it works great so far. Best Giovanni