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Alliance BLAST Database Manager

Requirements

Items marked with '(dev)' indicate dependencies that are only needed if running natively outside the Docker container.

  • Unix / OS X (x86_64 or arm64 platforms)
  • Docker
  • Python 3.10+ (dev)
  • Poetry (dev)
  • gunzip (dev)
  • xargs (dev)
  • makeblastdb - NCBI BLAST 2.12.0+ (dev)
  • git
  • wget (dev)
  • jq (formatting database metadata from MOD)

Getting Started

The following requires that you have Docker installed and running on your system. The make docker-build or make docker-buildx targets build the container image and the make docker-run runs the pipeline.

On x86_64

git clone https://github.com/alliance-genome/agr_blastdb_manager.git
cd agr_blastdb_manager
make docker-build
make docker-run
ls -l data/fasta/* data/blast/*

On arm64

git clone https://github.com/alliance-genome/agr_blastdb_manager.git
cd agr_blastdb_manager
make docker-buildx
make docker-run
ls -l data/fasta/* data/blast/*

make docker-buildx builds a multi-platform container.

  • Note: You may need to activate the custom docker builder with docker buildx create --use first.

Description

A Snakemake pipeline for automating the aggregation of model organism datasets and production of BLAST databases.

How to add a new model organism database

  1. Create a new databases.json file and place it in conf/<MOD_NAME>/databases.json. e.g. conf/flybase/databases.json.

See the [./conf/metadata_schema.json](metadata schema file) for full details on the format and other existing files for examples.

  1. Add a new entry under mods for the new configuration file to conf/global.yaml.

This tells Snakemake to process this file.

Follow the instructions under Getting Started.