IEDB / arborist

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Arborist

Arborist builds trees for the IEDB. The trees are used for the user interface on https://iedb.org and the IEDB curation interface, and also for validating IEDB data. They combine data from the IEDB with community ontologies such as the NCBI Taxonomy and open scientific databases such as UniProt and Genbank.

WARN: This version of Arborist is still work-in-progress. It makes extensive use of Nanobot, which is also work-in-progress.

Usage

The Makefile defines and documents all the specific steps for Arborist. Run make help to see the list of main tasks.

You can either run make directly or inside a Docker container. For Docker, run ./run_image.sh make or sudo -E ./run_image.sh make. If you aren't using Docker, first install the required software by running make deps. NOTE: Arborist currently supports only Linux on the x86_64 architecture.

The suggested workflow is:

  1. Update the cache with the latest IEDB tables by running src/iedb/update-cache. This requires MySQL/MariaDB connection parameters to be set as IEDBMYSQL* environment variables: IEDB_MYSQL_HOST, IEDB_MYSQL_PORT, IEDB_MYSQL_USER, IEDB_MYSQL_PASSWORD, IEDB_MYSQL_DATABASE.
  2. Run make all to build all trees.
  3. Run make serve to start the web interface on http://localhost:3000.

These are the key Make tasks for building trees, in their dependency order:

TODO: build more trees: peptide, molecule, assay, disease, geolocation, ...

Here are some other important Make tasks:

Files and Directories