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Docker image for eggNOG mapper
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get_kegg_reaction_metadata.py
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README.md

docker-eggnog-mapper

Docker image for eggNOG mapper

Docker Repository on Quay

This is a very thin wrapper around the eggNOG mapper tool. See https://github.com/jhcepas/eggnog-mapper for more details on that tool.

The main addition is the inclusion of a run_eggnog_mapper.py script, which handles:

  • Downloading the reference database from an S3 bucket
  • Writing the results to a local path or S3 bucket

There is also a script that will parse the eggNOG output and generate a SQLite database with all of the reaction metadata for the detected set of KEGG orthologs fetched from the KEGG API. The tables and columns are:

  • ortholog: [ortholog, name, definition]
  • reaction: [reaction, ortholog, definition, equation, enzyme]
  • compound: [compound, name, formula]
  • pathway: [pathway, reaction, name, class]

NOTE: The reaction table maps to all of the other tables, which in the case of the compound table is via the equation column, which contains compound entry names.

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