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nselem avatar nselem commented on August 20, 2024 1

Thank you for using the material. We do not use Kraken in the lesson since because of RAM limitations some laptops won't be able to run it. For that reason, we provide the report files from Kraken, and you only will need kraken-biom. Anyway, here is the biom file, which also should be available for future versions of the data in zenodo
https://github.com/carpentries-incubator/metagenomics/blob/gh-pages/files/cuatroc.biom

Some notes:

  1. The kraken output files are on the zenodo data as indicated in the data section
    https://carpentries-incubator.github.io/metagenomics-workshop/data/index.html

  2. The software can be installed using the yml specifications file indicated in the setup section

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samnooij avatar samnooij commented on August 20, 2024

Thank you for sharing the BIOM file! I just noticed that I had been looking at the setup page for the genomics workshop (https://datacarpentry.org/genomics-workshop/setup.html) instead of the one for the metagenomics workshop (https://carpentries-incubator.github.io/metagenomics-workshop/setup.html). My bad! I see the metagenomics setup page indeed includes all the software packages and a conda YAML file. That should settle the issues I ran into. Sorry if I caused some confusion.

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nselem avatar nselem commented on August 20, 2024

Please if you have time, let us know if the setup works for you. Thank you for using the lesson.

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