Prerequisites for the Enterprise Pipeline: /Documentation/Archive/9.1

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Install the Enterprise Pipeline

Prerequisites for the Enterprise Pipeline

Documentation: Version 9.1

Prerequisites for the Enterprise Pipeline

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NOTE: The documents for the Enterprise Pipeline are currently in draft form. They will be periodically updated.

In order to install the LabKey Enterprise Pipeline, you will first need to have the following prerequisite software installed and configured.

A Working Installation of the LabKey Server
JMS Queue (ActiveMQ)
Globus GRAM Server
Conversion Service (convert MS2 output to mzXML )

The Conversion Service is optional, and only required if you plan to convert files to mzXML format in your pipeline

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Install the Server

Access the Server

Set Up a Folder & its Tools

Learn User Basics

Learn Admin Basics

Extend LabKey Server

Learn What's New in 9.1

9.1 Upgrade Tips

Learn What's New in 9.2

9.2 Upgrade Tips

Tutorials and Online Demos

Webinars and Videos

Roadmap for the Future

Installs and Upgrades

Before You Install

Install LabKey via Installer

Install LabKey Manually

	Install Required Components
	Configure the Web Application
	Modify the Configuration File
	Supported Tomcat Versions
	Third-Party Components and Licenses
	Manual install of caBIG™

Upgrade PostgreSQL

Set Up MS Search Engines

Install the Enterprise Pipeline

Prerequisites for the Enterprise Pipeline

	RAW to mzXML Converters
	JMS Queue
	Globus GRAM Server
	Create a New Globus GRAM user

Configure LabKey Server to use the Enterprise Pipeline

	Edit and Test Configuration
	Using the Enterprise Pipeline
	Configure the Conversion Service

Troubleshooting the Enterprise Pipeline

Install the Perl-Based MS2 Cluster Pipeline

	Install the mzXML Conversion Service
	Run the MS2 Cluster Pipeline

Example Setups and Configurations

	Install CPAS on Linux
	Example Installation of Flow Cytometry on Mac OSX
	Configure FTP on Linux
	Configure R on Linux
	Configure the Virtual Frame Buffer on Linux

Draft Material for OpenSSO

Customize "Look and Feel"

Troubleshooting

Projects and Folders

Create Project or Folder

Customize Folder

Reasons to Choose a "Custom"-Type Folder

Set Permissions

Manage Project Members

Navigate Folder Hierarchy

Move/Rename/Delete/Hide

Access Module Services

Manage Web Parts

Establish Terms of Use for Project

Security and Accounts

Site Administrator

Hide Admin Menus

Anonymous Users

Security Groups

	Global Groups
	Project Groups
	Site Groups

How Permissions Work

Permission Levels for Roles

Test Security Settings by Impersonating Users

	Basic Authentication
	Single Sign-On Overview

Look & Feel Settings

Additional Methods for Customizing Projects (DEPRECATED)

Navigation Element Customization (DEPRECATED)

Email Notification Customization

Backup and Maintenance

Administering the Site Down Servlet

Application & Module Inventory

	XAR Tutorial Sample Files
	Describing Experiments in CPAS
	Xar.xml Basics
	Describing Protocols
	Describing LCMS2 Experiments

Overview of Life Sciences IDs

LSID Substitution Templates

Sub-Inventories

	Application Inventory
	Module Inventory
	Web Part Inventory (Basic Wiki Version)
	Web Part Inventory (Expanded Wiki Version)

Create a Collaboration Folder

	Using the Issue Tracker
	Administering the Issue Tracker

	Using the Message Board
	Administering the Message Board

Wiki Admin Guide

Wiki User Guide

Wiki Syntax Help

Advanced Wiki Syntax

Embed Live Content in Wikis

Web Part Configuration Properties

Wiki Attachment List

Set up the Demo Study

Set up Datasets and Specimens

Sort and Filter Grid Views

Create an R View

Create an R View with Cairo

Explore Specimens

Study Adminstrator Guide

	Directly Create Study
	Use Study Designer

Import/Export/Reload a Study

Study Import/Export Formats

Manage Datasets

Manage Labs and Sites

Manage Study Security

	Configure Permissions for Reports & Views
	Matrix of Dataset- and Folder-Level Permissions

Define and Map Visits

Advice on Defining Visits

Manually Create and Map Visits

	Create a Visit
	Edit Visits
	Map Visits
	Identify Visit Dates

Import Visits and Visit Map

Create and Populate Datasets

Direct Import Pathway

Create a Single Dataset

Create a Single Dataset and Schema

Create Multiple Datasets and Schemas

Dataset Properties

	Schema Field Properties
	Pre-Defined Schema Properties
	Date and Number Formats

Import Data Records

Import via Copy/Paste

Import From a Dataset Archive

Create Pipeline Configuration File

Assay Publication Pathway

Manage Your New Dataset

Set Up, Design & Copy Assays

Manage Specimens

	Import a Specimen Archive
	Import Specimens Via Cut/Paste
	Set Up Specimen Request Tracking
	Approve Specimen Requests

Create Reports And Views

	Advanced Views
	The Enrollment View
	Workbook Reports

Annotated Study Schema

Study User Guide

Site Navigation

Study Navigation

The Study Navigator

Selecting, Sorting & Filtering

Reports and Views

Dataset Import & Export

	Dataset Import
	Dataset Export

	Specimen Shopping Cart
	Specimen Reports

Wiki User Guide

Accounts and Permissions

	Password Reset & Security
	Permissions
	Your Display Name

Get Started With CPAS

Explore the MS2 Dashboard

Upload MS2 Data Via the Pipeline

Set Up MS2 Search Engines

Install SequestQueue

Set the LabKey Pipeline Root

Search and Process MS2 Data

Configure Common Parameters

Configure X! Tandem Parameters

Configure Mascot Parameters

Configure Sequest Parameters

	Sequest Parameters
	MzXML2Search Parameters
	Examples of Commonly Modified Parameters

Working with MS2 Runs

Viewing an MS2 Run

Customizing Display Columns

	Peptide Columns
	Protein Columns

Viewing Peptide Spectra

Viewing Protein Details

Viewing Gene Ontology Information

Comparing MS2 Runs

Exporting MS2 Runs

Loading Public Protein Annotation Files

Using Custom Protein Annotations

Using ProteinProphet

Using Quantitation Tools

Experimental Annotations for MS2 Runs

Exploratory Features

caBIG™-certified Remote Access API to LabKey/CPAS

Label-Free Quantitation

LabKey Flow Overview

Flow Team Members

Tutorial: Import a FlowJo Workspace

	Install LabKey Server and Obtain Demo Data
	Create a Flow Project
	Set Up the Data Pipeline and FTP
	Place Files on Server
	Import a FlowJo Workspace and Analysis
	Customize Your View
	Examine Graphs
	Examine Well Details
	Finalize a Dataset View and Export

Tutorial: Perform a LabKey Analysis

Create Custom Flow Queries

	Locate Data Columns of Interest
	Add Statistics to FCS Queries
	Calculate Suites of Statistics for Every Well
	Flow Module Schema

Add Sample Descriptions

Assay Administrator Guide

Set Up Folder For Assays

Design a New Assay

Property Fields

General Properties

ELISpot Properties

Luminex Properties

Microarray Properties

Edit Plate Templates

Copy Assay Data To Study

Copy-To-Study History

Tutorial: Import Microarray Data

	Install LabKey Server
	Create a Microarray Project
	Set Up the Data Pipeline and FTP

Assay User Guide

Import Assay Runs

Import General Assays

Import ELISpot Runs

Import Luminex Runs

Luminex Conversions

Import Microarray Runs

Import NAb Runs

Work With Assay Data

Dataset Grid Views

Participant Views

Selecting, Sorting & Filtering

	Select Data
	Sort Data
	Filter Data

Custom Grid Views

Create Custom Grid Views

Select and Order Columns

Example: Create a "Joined View" from Multiple Datasets

Pre-Define Filters and Sorts

Save and View Custom Views

Reports and Views

The R View Builder

Author Your First Script

Upload a Sample Dataset

Access Your Dataset

Determine Available Graphing Functions

Graphics File Formats

Use Input/Output Syntax

Work with Saved R Views

Display R View on Portal

Create Advanced Scripts

	Means, Regressions and Multi-Panel Plots
	Basic Lattice Plots
	Participant Charts
	User-Defined Functions

R Tutorial Video for v8.1

FAQs for LabKey R

Custom SQL Queries

	Create a Custom Query
	Use the Source Editor
	Use the Query Designer
	Review Metadata in SQL Source Editor
	Display a Query
	Add a Calculated Column to a Query
	Use GROUP BY and JOIN
	Use Cross-Folder Queries
	LabKey SQL Reference
	Metadata XML

Lists & External Schemas

	Lists
	External Schemas

File Upload and Sharing

	Set Up File Sharing
	Use File Sharing

	Set the LabKey Pipeline Root
	Set Up the FTP Server
	Upload Pipeline Files via FTP

Tutorial Video: Building Views and Custom User Interfaces

Client-Side APIs

Tutorial: JavaScript API

	Reagent Request Form
	Reagent Request Confirmation Page
	Summary Report for Reagent Managers

Licensing for the Ext API

Generate JavaScript

Example: Charts

JavaScript Class List

Java Class List

Setup Steps for SAS

Configure SAS Access From LabKey Server

Server-Side APIs

	Examples: Controller Actions
	Example: Access APIs from Perl

How To Find schemaName, queryName & viewName

Web Part Configuration Properties

Implementing API Actions

Programmatic Quality Control

Using Java for Programmatic QC Scripts

Developer Documentation

Recommended Skill Set

Setting up a Development Machine

	Notes on Setting up a Mac for LabKey Development
	Machine Security
	Enlisting in the Version Control Project
	Source Code

Confidential Data

Development Cycle

Project Process

Release Schedule

Submitting Contributions

Checking Into the Source Project

Developer Email List

Wiki Documentation Tools

The LabKey Ontology & Query Services

Building Modules

Third-party Modules

Module Architecture

Simplified Modules

	Queries, Views and Reports in Modules
	Assays defined in Modules

Getting Started with the Demo Module

Creating a New Module

Deprecated Components

The LabKey Server Container

CSS Design Guidelines

Maintaining the Module's Database Schema

Integrating with the Pipeline Module

Integrating with the Experiment Module

GWT Integration

GWT Remote Services

UI Design Patterns

LabKey Server and the Firebug add-on for Firefox

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