1. Install VirtualBox
, Vagrant
, and Ansible
.
2. Configure variables in playbook:
$ ${EDITOR} pergenie/deploy/playbook/group_vars/staging # e.g. pergenie/deploy/playbook/group_vars/example/staging.example
3. Build VM and deploy:
$ cd pergenie/deploy
$ vagrant up
Once VM is up, you can rollout pergenie application by:
$ ANSIBLE_TAGS=rollout vagrant provision
See details in pergenie/deploy
1. Install requirements
- Python >=2.7,<3
- PostgreSQL
- RabbitMQ
2. Install Python packages
$ pip install -r requirements/development.txt
3. Configure settings.py
$ ${EDITOR} pergenie/settings/development.py # e.g. pergenie/settings/development.py.example
4. Create PostgreSQL user and database
$ createuser pergenie --password
$ createdb pergenie -O pergenie
5. DB migration
$ python manage.py migrate
6. Init data
$ python manage.py createsuperuser
$ python manage.py update_gwascatalog
$ python manage.py setup_go_vcf_tools
$ python manage.py init_demo_user
7. Run Celery for job queing
$ DJANGO_SETTINGS_MODULE=pergenie.settings.development celery --app=pergenie worker
8. Run development server
$ python manage.py runserver
9. Browse application at http://127.0.0.1:8000/
Versions of public data resources are pinned as follows:
Resources | Versions |
---|---|
Human Reference Genome | GRCh37p13 |
dbSNP | b144 |
-
Currently, main design data (
static/vendor/wood-admin/stylesheets/application.css
) is not included in this repository. You can purchase from wrapbootstrap.com/theme/wood-admin-theme-WB0941911. Sorry for inconvenience. -
Following open source stylesheet/image/javascript products are used under the each license:
- Bootstrap, Apache License v2.0
- Highcharts JS, for free under the Creative Commons Attribution-NonCommercial 3.0 License
- jQuery, MIT License
- jQuery MultiFile, MIT License
- Peity, MIT License
- Intro.js, MIT License
- google/code-prettify, Apache License v2.0
See LICENSE