Chapter 1. Building EMBOSS
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Chapter 1. Building EMBOSS
Table of Contents
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