This repo contains a number of Hail utility functions and scripts for the gnomAD project and the MacArthur lab. Load using:
from gnomad_hail.resources import *
from gnomad_hail.utils import *
from gnomad_hail.slack_utils import *
Resource map
Hail helper functions
Helper functions for posting to Slack.
Submit along with slack_creds.py
(e.g. in HAIL_SCRIPTS
environment variable in pyhail.py
) which has only a slack_token
variable with a Slack API key.
Submission script for Hail. Notable differences from cloudtools include:
- Inline scripts (
--inline "print hc.read('gs://bucket/my.vds').count()"
) - Add helper scripts designated in
HAIL_SCRIPTS
environment variable
Google Cloud initialization scripts.
Cluster should be started up with --init gs://gnomad-public/tools/inits/master-init.sh
, which is tracked here, deployed to cloud for usage.
gnomad-init.sh
and sparklyr-init.sh
are pulled from this repo and called by master-init.sh
.
Tests are run automatically on creation of each cluster (in gnomad-init.sh
) and can be triggered manually using:
cd /path/to/gnomad_hail
PYTHONPATH=.:$PYTHONPATH python -m unittest discover