The server side application of the BRowse All Variants Online (BRAVO) project.
For running an instance of Bravo API, install as a package.
python -m pip install git+https://github.com/statgen/bravo_api.git@main
See Development section for developer installation.
#!/bin/sh
# Example run script for local development
# Activate venv if present.
[ -d 'venv' ] && source 'venv/bin/activate'
export FLASK_ENV=development
export FLASK_APP=bravo_api
# Confige file is relative to the instance directory.
export BRAVO_API_INSTANCE_DIR='/var/local/bravo/instance'
export BRAVO_API_CONFIG_FILE='config.py'
flask run --port 9090Or use gunicorn in production instead of flask run
gunicorn -b 127.0.0.1:9090 -w 5 -k gevent "bravo_api:create_app()"The runtime data on disk needs to be present before running.
/var/local/bravo/data
└── runtime
├── cache
├── coverage
├── crams
└── reference
The paths to the runtime data needs to be specified in the config.py
BASE_DIR = os.path.join(os.sep, 'var', 'local', 'bravo', 'data', 'runtime')
COVERAGE_DIR = os.path.join(BASE_DIR, 'coverage')
SEQUENCES_DIR = os.path.join(BASE_DIR, 'crams')
SEQUENCES_CACHE_DIR = os.path.join(BASE_DIR, 'cache')
REFERENCE_SEQUENCE = os.path.join(BASE_DIR, 'reference', 'chr11_hs38DH.fa')MongoDB needs to be pupulated with the basis data prior to running the api.
/var/local/bravo/data/basis/
├── qc_metrics
│ └── metrics.json.gz
├── reference
│ ├── canonical_transcripts.tsv.gz
│ ├── gencode.v38.annotation.gtf.gz
│ ├── hgcn_genenames.tsv.gz
│ └── omim_ensembl_refs.tsv.gz
└── vcfs
├── chr11.bravo.vcf.gz
└── chr11.bravo.vcf.gz.tbi
The package provides commands to load the basis data.
venv/bin/flask load-genes \
data/basis/reference/canonical_transcripts.tsv.gz \
data/basis/reference/omim_ensembl_refs.tsv.gz \
data/basis/reference/hgcn_genenames.tsv.gz \
data/basis/reference/gencode.v38.annotation.gtf.gz
venv/bin/flask load-snv 2 data/basis/vcfs/*.vcf.gz
venv/bin/flask load-qc-metrics
data/basis/qc_metrics/metrics.json.gzThe pysam wheel provided from pypi does not include S3 support. Pysam needs to be build with the "--enable-s3" option.
HTSLIB_CONFIGURE_OPTIONS="--enable-s3"
pip install pysam --force-reinstall --no-binary :all:Checkout and install as editable package with development and testing extras.
git clone https://github.com/statgen/bravo_api.git
cd bravo_api
python -m pip install -e .[dev,test]
When installed as editable package, run pytest from root dir or anywhere in tests dir.
# Run the tests
pytest
Top level testconf.py in the tests directory prevents marked tests from running. In order to run marked tests in addition to the unmarked, provide a match expression.
# Run integration tests
pytest -m 'integration'
A low overhead (not constantly polling) method of running pytest anytime a .py file is changed
can be achieved using fd and entr in a separate terminal.
Only thing this won't pick up is new files.
fd '.*\.py$' | entr -c pytestSee notes.md