Hello all, I am working in the community analysis of the metagenomics data. Kraken2 is complied and merge all its previous separate tools to run in Galaxy. The problem i am facing is that, it will not generate file to view results in the Krona Pie chart. It is most essential step to visualize the …

Good morning, You can convert Kraken data to a format compatible with Krona by using the Convert Kraken data to Galaxy taxonomy representation tool, available at usegalaxy.org and .eu, as well as installable from the toolshed . I haven’t checked whether it’s compatible with kraken2 output, but since…

That tool supports the kraken results… It is not working for the results of Kraken2.

Good to know. We’ll have to create one for Kraken2, then.

Hi , I am trying to install kraken2 databases through data manger. Its giving me an URL error to download the databases. Can you please check if the URL provided is correct?. here is the error: Fatal error: Exit code 1 () Possible unintended interpolation of @2 in string at /dep/_conda/envs/__kra…

Hi - You are using the version from the Test ToolShed. Tools there are for development (only) and can present with many problems. You’ll need to either consider using the original Kraken tools/DM or wait for the Kraken2 DM to be ready. I don’t have an issue ticket yet for you to track but will chec…

Hi @JayanthiG , the kraken2 data manager is a work-in-progress. When it’s complete, it will be uploaded to the main toolshed under ownership of the iuc (Intergalactic Utilities Commission) group. My progress on the data manager can be viewed on this pull request: [dfornika] [W…

@JayanthiG I’ve attempted to update the test toolshed but it appears that it is already up-to-date. The latest revision is 29:65cbfb5e6f65 from 2019-03-29. Based on your error message, it looks like the URL that was being used to download the minikraken database is invalid. I’ve just looked at the …

@JayanthiG I’ve updated the URL in the data manager and pushed the update to both my GitHub pull-request and to the Test Toolshed. The latest revision ( 30:0aaff8fb824d ) should pull the minikraken2 database from the correct location now.

Thanks so much Dan. Appreciate your help on it!. Jayanthi

Galaxy Community Help

How to view Kraken2 Results in Krona?

usegalaxy.org support

troubleshooting

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