From c1051e4d92f8e5b7a275ab983aad94b96ba9f4e5 Mon Sep 17 00:00:00 2001
From: Ino de Bruijn <ino@ino.pm>
Date: Tue, 27 Nov 2018 14:27:41 -0500
Subject: [PATCH] Add files for config of gitbook.com

---
 book.json       |  3 +++
 docs/SUMMARY.md | 61 +++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 64 insertions(+)
 create mode 100644 book.json
 create mode 100644 docs/SUMMARY.md

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+{
+    "root": "./docs"
+}
diff --git a/docs/SUMMARY.md b/docs/SUMMARY.md
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+# Summary
+
+## 1. General
+* [News](News.md)
+* [Frequently Asked Questions](FAQ.md)
+* [About Us](About-Us.md)
+* [List of RFCs](RFC-List.md)
+
+## 2. cBioPortal Deployment
+### 2.1 Deployment
+* [Hardware and Software Requirements](System-Requirements.md)
+* [Pre-Build Steps](Pre-Build-Steps.md)
+* [Building from Source](Build-from-Source.md)
+* [Importing the Seed Database](Import-the-Seed-Database.md)
+* [Loading a Sample Study](Load-Sample-Cancer-Study.md)  
+* [Deploying the Web Application](Deploying.md)
+
+### 2.2 Authorization and Authentication
+* [User Authorization](User-Authorization.md)
+* [Authenticating Users via SAML](Authenticating-Users-via-SAML.md)
+* [Authenticating Users via LDAP](Authenticating-Users-via-LDAP.md)
+* [Authenticating and Authorizing Users via Keycloak](Authenticating-and-Authorizing-Users-via-keycloak.md)
+
+### 2.3 Customization 
+* [Customizing your cBioPortal Instance via portal.properties](Customizing-your-instance-of-cBioPortal.md)
+* [More portal.properties Settings](portal.properties-Reference.md)
+
+### 2.4 Docker
+* [Docker Prerequisites](Docker-Prerequisites.md)
+* [Deploy using Docker](Deploy-Using-Docker.md)
+* [Uninstall Docker cBioPortal](Uninstall-Docker-cBioPortal.md)
+* [Import a Study Using Docker](Import-Study-Using-Docker.md)
+
+## 3. cBioPortal Maintenance
+* [Updating your cBioPortal Database Scheme](Updating-your-cBioPortal-installation.md)
+* [Update genes and gene aliases](Updating-gene-and-gene_alias-tables.md)
+
+## 4. Development      
+* [cBioPortal Entity-relationship Diagram](cBioPortal-ER-Diagram.md)
+* [Using the Data Manager to Get Data and Set Session Parameters](Data-Manager.md)
+* [Accessing Services via the Web-API](cBioPortal-Web-API.md)
+   * [API and API Client](The-API-and-API-Client-[Beta].md)
+* [Providing cBioPortal Parameters](providing-cBioPortal-parameters.md)
+* [Manual test cases](manual-test-cases.md)
+
+## 5. Data Loading
+### 5.1 Data Loading
+* [Data Loading Overview](Data-Loading.md)
+   * [Using the Dataset Validator](Using-the-dataset-validator.md)
+   * [Using the metaImport Script](Using-the-metaImport-script.md)
+   * [Development, Debugging and Maintenance Using cbioportalImporter](Development,-debugging-and-maintenance-mode-using-cbioportalImporter.md)
+   * [File Formats](File-Formats.md)
+       * [Z-Score Normalization](Z-Score-normalization-script.md)
+   * [Data Loading: How the loader deals with Hugo Symbols](Data-Loading-How-the-loader-deals-with-Hugo-symbols.md) (TODO)    
+   * [Data Loading: What You Need To Change](Data-Loading-What-You-Need-To-Change.md)
+   * [Data Loading: Tips and Best Practices](Data-Loading-Tips-and-Best-Practices.md)
+   * [Importer Tool](Importer-Tool.md) (deprecated)
+   * [Importing Gene Sets](Import-Gene-Sets.md)
+
+### 5.2 Datasets
+* [Downloads](Downloads.md)