SAS Security: /Documentation/Archive/9.1

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SAS Security

Documentation: Version 9.1

SAS Security

The SAS library performs all requests to the LabKey Server under a given user account with all the proper security enforced on the server. User credentials are obtained from a separate location than the running SAS program so that SAS programs may be shared without compromising security.

As in the Rlabkey package, user credentials are read from a file in the user’s home directory, so as to keep those credentials out of SAS programs, which may be shared between users. Most Unix Internet tools already use the .netrc file, so the LabKey SAS library also uses that file.

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Before You Install

Install LabKey via Installer

Install LabKey Manually

	Install Required Components
	Configure the Web Application
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	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
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	Configure R on Linux
	Configure the Virtual Frame Buffer on Linux

Draft Material for OpenSSO

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Overview of Life Sciences IDs

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Create Pipeline Configuration File

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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

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Working with MS2 Runs

Viewing an MS2 Run

Customizing Display Columns

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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
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	Finalize a Dataset View and Export

Tutorial: Perform a LabKey Analysis

Create Custom Flow Queries

	Locate Data Columns of Interest
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	Calculate Suites of Statistics for Every Well
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Add Sample Descriptions

Assay Administrator Guide

Set Up Folder For Assays

Design a New Assay

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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

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Author Your First Script

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R Tutorial Video for v8.1

FAQs for LabKey R

Custom SQL Queries

	Create a Custom Query
	Use the Source Editor
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	Review Metadata in SQL Source Editor
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	Use GROUP BY and JOIN
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	Metadata XML

Lists & External Schemas

	Lists
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File Upload and Sharing

	Set Up File Sharing
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	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

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Java Class List

Setup Steps for SAS

Configure SAS Access From LabKey Server

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	Examples: Controller Actions
	Example: Access APIs from Perl

How To Find schemaName, queryName & viewName

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Using Java for Programmatic QC Scripts

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The LabKey Server Container

CSS Design Guidelines

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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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