EMBOSS Administrators Guide
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EMBOSS Administrators Guide

Bioinformatics Software Management

Dr. Alan Bleasby

Senior Scientific Officer
EMBL European Bioinformatics Institute

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

Dr. Jon Ison

Senior Scientific Officer
EMBL European Bioinformatics Institute

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

Mr. Peter Rice

Group Leader
EMBL European Bioinformatics Institute

EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

Revision History
August 2009The EMBOSS Developers
Version 1

Table of Contents

Acknowledgements
1. EMBOSS Acknowledgements
1.1. Funding Bodies
1.2. Contributors
2. EMBOSS Administrators Guide Acknowledgements
Preface
1. Introduction to EMBOSS
2. Administration of EMBOSS
3. About the Authors
4. How To Cite EMBOSS
Conventions
1. Command Line Sessions and Commands
2. Program Listings and Code
3. Other Conventions
4. Special Text Blocks
Welcome to the EMBOSS Administrators Manual
1. Chapter 1. Building EMBOSS
2. Chapter 2. Building EMBASSY
3. Chapter 3. Building Jemboss
4. Chapter 4. Databases
5. Appendix A. Resources
6. Appendix B. Frequently Asked Questions (FAQ)
1. Building EMBOSS
1.1. Downloading EMBOSS
1.1.1. Downloading with a Web Browser
1.1.2. Downloading by Anonymous FTP
1.1.2.1. Interactive FTP
1.1.2.2. FTP using wget
1.1.3. Unpacking the Source Code
1.2. Building EMBOSS
1.3. Configuring EMBOSS
1.3.1. A Simple Configuration
1.3.2. Configuring EMBOSS to use Graphics
1.3.3. Configuring with PNG Graphics
1.3.4. Configuring with PDF Graphics
1.3.5. Configuration, Ensembl and SQL
1.3.6. If you need to Configure Again
1.3.7. Advanced Configuration Options
1.3.8. Configuration Options to Avoid
1.3.9. Configuration Options to Use
1.4. Compiling EMBOSS
1.4.1. Reporting Compilation Errors
1.5. Installing the Libraries and Applications
1.6. Post-installation of EMBOSS
1.6.1. Testing the EMBOSS Installation
1.6.1.1. Common Errors During Testing
1.6.2. Post-installation of Data Files
1.6.2.1. REBASE
1.6.2.2. AAINDEX
1.6.2.3. PRINTS
1.6.2.4. PROSITE
1.6.2.5. JASPAR
1.6.3. Deleting the EMBOSS Package
1.6.4. Keeping EMBOSS Up To Date
1.6.5. Installing a New Version of EMBOSS
1.6.6. EMBOSS Configuration Files
1.6.6.1. Syntax of emboss.default and .embossrc Files
1.6.6.2. Configuring EMBOSS for Different Groups of Users
1.6.7. EMBOSS Environment Variables
1.6.7.1. Global Qualifiers
1.6.7.2. Logging
1.6.7.3. Environment Variables File (variables.standard)
1.6.8. EMBOSS Data Files
1.7. EMBOSS Installation: Platform-specific Concerns
1.7.1. Linux RPM Distributions
1.7.1.1. General Prerequisites
1.7.1.2. PNG prerequisites
1.7.1.3. PDF prerequisites
1.7.1.4. Java
1.7.2. Linux Debian Distributions
1.7.2.1. General Prerequisites
1.7.2.2. PNG prerequisites
1.7.2.3. PDF prerequisites
1.7.2.4. Java
1.7.3. MacOSX
1.7.3.1. General Prerequisites
1.7.3.2. PNG prerequisites
1.7.3.3. PDF prerequisites
1.7.3.4. Java
1.7.4. IRIX
1.7.4.1. General Prerequisites
1.7.4.2. PNG prerequisites
1.7.4.3. PDF prerequisites
1.7.4.4. Java
1.7.5. Tru64
1.7.5.1. General Prerequisites
1.7.5.2. PNG prerequisites
1.7.5.3. PDF prerequisites
1.7.5.4. Java
1.7.6. Solaris
1.7.6.1. General Prerequisites
1.7.6.2. PNG prerequisites
1.7.6.3. PDF prerequisites
1.7.6.4. Java
1.8. Troubleshooting EMBOSS Installations
1.9. PNG support: Installing from Source Code
1.9.1. LIBPNG Compilation
1.9.2. gd Compilation
1.10. PDF support: Installing from Source Code
1.11. Ncurses Support: Installing from Source Code
1.11.1. Ncurses Compilation
2. Building EMBASSY
2.1. Introduction to EMBASSY
2.2. Downloading the EMBASSY Packages
2.2.1. Unpacking the Source Code
2.3. Building the EMBASSY Packages
2.4. Configuring the EMBASSY Packages
2.4.1. A Simple Configuration
2.4.1.1. CBSTOOLS
2.4.1.2. DOMAINATRIX
2.4.1.3. DOMALIGN
2.4.1.4. DOMSEARCH
2.4.1.5. EMNU
2.4.1.6. ESIM4
2.4.1.7. HMMER
2.4.1.8. IPRSCAN
2.4.1.9. MEME
2.4.1.10. MIRA
2.4.1.11. MSE
2.4.1.12. MYEMBOSS
2.4.1.13. MYEMBOSSDEMO
2.4.1.14. PHYLIP
2.4.1.15. SIGNATURE
2.4.1.16. STRUCTURE
2.4.1.17. TOPO
2.4.1.18. VIENNA
2.5. Compiling the EMBASSY Packages
2.5.1. Reporting Compilation Errors
2.6. Installing the EMBASSY Packages
2.7. Post-installation of the EMBASSY Packages
2.7.1. Testing an EMBASSY Installation
2.7.2. Deleting an EMBASSY Package
2.7.3. Keeping EMBASSY up to Date
2.7.4. Reinstallation of EMBASSY and EMBOSS
2.8. EMBASSY Installation: Platform-specific Concerns
2.8.1. Linux RPM Distributions
2.8.1.1. General Prerequisites
2.8.1.2. Ncurses prerequisites
2.8.2. Linux Debian Distributions
2.8.2.1. General Prerequisites
2.8.2.2. Ncurses prerequisites
2.8.3. MacOSX
2.8.3.1. General Prerequisites
2.8.3.2. Ncurses prerequisites
2.8.4. IRIX
2.8.4.1. General Prerequisites
2.8.4.2. Ncurses prerequisites
2.8.5. Tru64
2.8.5.1. General Prerequisites
2.8.5.2. Ncurses prerequisites
2.8.6. Solaris
2.8.6.1. General Prerequisites
2.8.6.2. Ncurses prerequisites
3. Building Jemboss
3.1. Introduction to Jemboss
3.1.1. Jemboss as a Client/Server
3.1.2. Jemboss as a standalone GUI
3.2. Installing as a Standalone GUI
3.2.1. Prerequisites
3.2.2. Current Software Versions
3.2.3. Compiling EMBOSS for use with the Standalone Jemboss
3.2.4. Post-installation of the Standalone GUI
3.3. Installing as an Authenticating Client Server
3.3.1. Prerequisites
3.3.2. Current Software Versions
3.3.3. Client-Server Installation
3.3.3.1. Setting-up EMBASSY Packages
3.3.3.2. Installing Tomcat and Axis
3.3.3.3. Adding EMBASSY Packages to the Server (post-installation)
3.4. Installing as a Non-authenticating Client Server
3.5. Technical Details of Authentication
3.6. Starting and Stopping the Jemboss Server
3.6.1. Creating a Web Launch Page for the Jemboss Authenticating Server
3.7. What to do if your Certificates Expire
3.8. The jemboss.properties File
3.9. Setting up Jemboss to use Batch Queuing Software
3.10. Setting up the Clients
3.11. Troubleshooting JEMBOSS Installation
3.12. Jemboss Installation: Platform-specific Concerns
3.12.1. MacOSX
3.12.1.1. General Prerequisites
3.12.1.2. When Running the Script
3.12.2. IRIX
3.12.2.1. General Prerequisites
3.12.2.2. When Running the Script
4. Databases
4.1. General Database Configuration
4.1.1. Sequence Database Support
4.1.1.1. Query Levels, Access Methods and Attributes
4.1.2. Configuring EMBOSS to work with Databases
4.1.3. Example Database Definition File (emboss.default.template)
4.1.4. Test Databases
4.1.5. Testing your Database Definitions
4.2. Database Attributes
4.2.1. Introduction
4.2.2. Description of Attributes
4.2.2.1. method, methodall, methodentry, methodquery
4.2.2.2. format, formatentry, formatquery, formatall
4.2.2.3. type
4.2.2.4. fields
4.2.2.5. directory
4.2.2.6. filename
4.2.2.7. exclude
4.2.2.8. indexdirectory
4.2.2.9. url
4.2.2.10. proxy
4.2.2.11. httpversion
4.2.2.12. app, appentry, appquery, appall
4.2.2.13. dbalias
4.2.2.14. comment
4.2.2.15. release
4.2.2.16. hasaccession
4.2.2.17. caseidmatch
4.3. Database Access Methods
4.3.1. Introduction
4.3.2. Description of Database Access Methods
4.3.2.1. EMBOSS
4.3.2.2. EMBLCD
4.3.2.3. SRS
4.3.2.4. SRSFASTA
4.3.2.5. SRSWWW
4.3.2.6. BLAST
4.3.2.7. EMBOSSGCG
4.3.2.8. GCG
4.3.2.9. DIRECT
4.3.2.10. URL
4.3.2.11. APP
4.3.3. Mixed Access Methods
4.3.4. Database Farms
4.4. Miscellaneous Database Integration
4.4.1. REBASE
4.4.2. TRANSFAC
4.4.3. PROSITE
4.4.4. PRINTS
4.4.5. AAINDEX
4.4.6. CUTG
4.4.7. JASPAR
4.4.8. Miscellaneous Data Files
4.5. Database Indexing
4.5.1. Introduction
4.5.2. Resource Definitions, Cachesize and Pagesize
4.5.3. Indexing and Configuration
4.5.3.1. Flatfile Databases
4.5.3.2. GCG Format Databases
4.5.3.3. BLAST Databases
4.5.3.4. FASTA Databases
4.5.3.5. Other Databases
4.5.4. Configuring EMBOSS to use SRS for Database Look-up
4.5.5. Size of the dbx* Indexes
A. Resources
A.1. Software Distributions that Include EMBOSS
A.1.1. RPM Package Manager Files
A.1.2. Ports and Packages
B. EMBOSS Frequently Asked Questions

List of Tables

1.1. Environment variables
1.2. Environment variables associated with global qualifiers.
1.3. Environment variables to launch external applications.
4.1. Attributes used to Specify a Database
4.2. Database Access Methods
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   Acknowledgements