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Admin/SampleTracking/Demo

Galaxy Demos


This page contains instructions on how to setup Galaxy for various feature demos.

Sample Tracking Demo

The sample tracking demo script (download) creates all the necessary infrastructure to create sequencing requests in a laboratory environment. This script drops the current database and creates a new database with the same name. Then it does all the sample tracking prep work like:

  • Creates admin users based on the list in the Galaxy config file and a regular user (customer@corp.com)

  • Creates a data library named 'DemoDataLib'

  • Sets permissions on the library so that all the users have been granted ADD/MODIFY/MANAGE PERMISSIONS on the data library & its folders

  • Creates two form definitions (DemoRequestForm & DemoSampleForm) from the csv files provided as the command line parameters - see setup_lims_demo.sh

  • Creates a request type with the above mentioned forms and 3 states (New, Received & Done)

Requirements

This script assumes Galaxy is using PostgreSQL for database storage.

Warning

This script will delete the existing PostgreSQL database specified in the Galaxy config file universe_wsgi.ini. Be sure to change the database name in the database_connection config variable if you do not want the current Galaxy database to be deleted.

Instructions

Follow the steps below:

  1. Download the script tarball

  2. Untar the tarball in the Galaxy root directory. The tarball contains 4 files:
    1. setup_lims_demo.sh

    2. setup_lims_demo.py

    3. requestfd.csv

    4. samplefd.csv

  3. From the Galaxy root directory run:  $ sh setup_lims_demo.sh