Skip to content

Latest commit

 

History

History
55 lines (38 loc) · 1.16 KB

MAINTENANCE.md

File metadata and controls

55 lines (38 loc) · 1.16 KB

HIVFacts Data Maintenance

Dependencies

  1. Read access to HIVDB2 database (default: 127.0.0.1:3308/HIVDB2). Can be changed by specifying environment parameter DATABASE_URI. Check hivdbql/config.py (in private repo) for more information.
  2. Read/write access to HIVDB_Rules database (default: 10.77.6.244:3306/HIVDB_Rules). Can be changed by specifying environment parameter DATABASE_URI_HIVRULES.
  3. Python 3.7 runtime + pipenv. Run this command at the root directory: pipenv install.

data/aapcnt

To update this folder, run this command:

scripts/update-aapcnt.sh

data/codonpcnt

To update this folder, run this command:

scripts/update-codonpcnt.sh

data/apobecs

To update this folder, run following commands:

scripts/prepare-apobec-data.sh
scripts/update-apobec.sh

data/drm_hiv1.json

List of HIV-1 drug resistance mutation based on latest HIVDB algorithm.

scripts/update-drmlist.sh

data/sdrm_hiv1.json

List of HIV-1 drug resistance mutation based on latest HIVDB algorithm.

scripts/update-sdrmlist.sh

HIVDB algorithm in data/algorithms

TODO