This updates the plugin to be compatible with the IRIDA 21.01 metadata storage system (#11 ). This also updates the version of all the tools (staramr, rgi, and shovill) and adds code to extract and store more data within the IRIDA metadata system.
Testing
To test out you will need to start up an instance of Galaxy (e.g., by using docker run -d -p 48888:80 -v /path/to/irida/data:/path/to/irida/data phacnml/galaxy-irida-20.05).
Next you will need to install the appropriate tools in Galaxy. These are listed in the README file but are (staramr==0.7.1+galaxy2, rgi==5.1.1, and shovill==1.1.0+galaxy0).
This updates the plugin to be compatible with the IRIDA
21.01metadata storage system (#11 ). This also updates the version of all the tools (staramr, rgi, and shovill) and adds code to extract and store more data within the IRIDA metadata system.Testing
To test out you will need to start up an instance of Galaxy (e.g., by using
docker run -d -p 48888:80 -v /path/to/irida/data:/path/to/irida/data phacnml/galaxy-irida-20.05).Next you will need to install the appropriate tools in Galaxy. These are listed in the README file but are (
staramr==0.7.1+galaxy2,rgi==5.1.1, andshovill==1.1.0+galaxy0).You will then need to go through the steps necessary to build this plugin (https://github.com/phac-nml/irida-plugin-amr-detection/tree/update/plugin#installing-irida-libraries) and copy the resulting JAR file to
/etc/irida/plugins.Once this is done you can start up IRIDA, upload a sample (e.g., the one mentioned here https://github.com/phac-nml/irida-plugin-amr-detection/tree/update/plugin#tutorial-data), and run the AMR Detection pipeline.