blast-db-configuration

Description

Code for generating the Alliance BLAST DB configuration file for FlyBase

Requirements

• Poetry
• pre-commit

Getting Started

git clone [email protected]:FlyBase/blast-db-configuration.git
cd blast-db-configuration
poetry install
pre-commit install

Generating FlyBase BLAST Configuration

The following commands will generate a BLAST database configuration for all organisms listed in the organisms.json file.

poetry run generate --release <FB_RELEASE> --dmel-annot-release <DMEL_ANNOT_VERSION>

e.g

poetry run generate --release FB2024_02 --dmel-annot-release r6.57

See poetry run generate --help for a full list of supported options.

GitHub Action

The GitHub action workflows described below do the following:

• Create or update a BLAST DB configuration file
• Create a PR with the resulting changes
• Pull the changes from FlyBase into the Alliance BLAST DB repo
• Create a PR for the Alliance to review and act on

Procedure

Generate FlyBase Configuration

1. Visit the Actions tab for the repo.
2. Click on the Generate FlyBase BLAST Configuration workflow.
3. Click "Run workflow" and enter in the FlyBase release and Dmel annotation version number (e.g. FB2024_02 and r6.57).
4. After the workflow has run, there will be a pull request with the resulting configuration file. Review the pull request changes and merge if all looks good.

Copy Configuration to the Alliance

1. Visit the Actions tab for the Alliance BLAST configurations.
2. Click on the Update FlyBase Configuration workflow.
3. Click "Run workflow" and enter in the FlyBase release (e.g. FB2024_04). This is only used for the pull request text.
4. Review the pull request changes and follow the Alliance procedures.