Overview

HTTPS SSH
Description:
SMITH (Sequencing Machine Information Tracking and Handling) is a laboratory information management system (LIMS) with integrated workflow subsystem.

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Admin guide:

Requirements for the source:
-Maven (http://maven.apache.org/)
-NetBeans is a recommended IDE (https://netbeans.org/)
-PrimeFaces (http://primefaces.org/)
-Hibernate (http://hibernate.org/)

Requirements for the application:
-Java 6 (or higher) (http://www.java.com/)
-SMITH application to deploy
-MySql server (http://www.mysql.com/)
-MySql Workbench for MySql manipulation (optional) ((http://www.mysql.com/))
-Glassfish (https://glassfish.java.net/)


How to run the application (for admins).
1. Make sure that user with your login and password is in the src/main/setup/dump.sql in the User table (done by default)
2. Make sure the same login listed in src/main/webapp/WEB-INF/glassfish-web.xml (done by default)
3. Add the user to Glassfish file realm(http://docs.oracle.com/cd/E19159-01/820-1072/6ncp48v4e/index.html) (for the first time user admin with the password adminadmin is enough)
4. Run mysql server, create the database from src/main/setup/dump.sql (just execute the queries). Setup user/password, name and address of the database as it is written in src/main/resources/hibernate.cfg.xml and grant the privileges to the user
5. Deploy SMITH application to Glassfish

The workflow subsystem is dependant on the data structures of the IEO, yet, the Galaxy configuration files and running scripts can be found in src/main/setup/workflows/. If you want to setup similar workflow subsystem, please, contact the developers

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The MIT License (MIT)

Copyright (c) 2014-2016 IIT@SEMM

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.