Web console for accessing database of NGSV.

• Python (v2.7)
  • ngsv-tools
  • Flask
  • Flask-SQLAlchemy
  • gevent
  • gevent-websocket
  • Celery
  • SQLAlchemy
• MySQL
• RabbitMQ

$ git clone git@github.com:xcoo/ngsv-tools.git
$ cd ngsv-tools
$ python setup.py install

NGSV Console cannot create database. First, create database using ngsv-tools.

$ ngsv initdb [--dbuser DBUSER] [--dbpassword DBPASSWORD]

Setup configuration.

$ cp config/ngsv.ini.example config/ngsv.ini

[db]
host=mysql_host
user=mysql_user
password=mysql_password
db_name=ngsv

[console]
debug=False
testing=False

upload_dir=/path/to/upload_dir/
upload_dir_url=http://example.com/upload_files/

host=example.com

Start MySQL and RabbitMQ.

Start Celery.

$ celery worker --app=ngsvconsole.taskserver.celery -l info

Start web server

$ ./run.py --wsgi

Browse http://localhost:5000. And upload bam/bed files.

You cannot load human genome data into database on NGSV Console. Load cytobands and refgenes into MySQL database by the following commandline ngsvtools.

$ ngsv loadcytoband [--dbuser USER] [--dbpassword PASSWORD]
$ ngsv loadrefgene [--dbuser USER] [--dbpassword PASSWORD]

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.

You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.