GeneId Installation

How to install geneid

Table of contents:

1. Extracting the distribution
2. Geneid file listing
3. Compiling geneid code
4. INDEX

Extracting the distribution

geneid distribution contains several directories and files. Source code and documentation files are included in the distribution, as well as parameters file and other extra information.

The distribution os archived and compressed in a single file using the Linux command tar -zcvf. The compressed filename is geneid.tar.gz. geneid files can be extracted following these instructions:

- gzip -d geneid.tar.gz
- tar -xvf geneid.tar

Under Linux, try:

- tar -zxvf geneid.tar.gz

After executing those commands, the directory geneid will have been created in your current working directory.

Geneid file listing

geneid distribution contains the following things:

• bin/
  binaries will be stored over there.
• docs/
  HTML documentation. Open the index.html page.
• include/
  geneid header file called geneid.h.
• objects/
  object files will be stored over there.
• params/
  Different parameters files are provided. Select the proper one according to the organism to which the input sequence belongs.
• samples/
  Some FASTA sequences as examples (E. Blanco, G. Parra and R. Guig�. Using geneid to Identify Genes. In A. D. Baxevanis and D. B. Davison, chief editors: Current Protocols in Bioinformatics. Volume 1, Unit 4.3. John Wiley & Sons Inc., New York, 2002. ISBN: 0-471-25093-7.)
• src/
  geneid source code.
• GNULicense
  This software has been registered under this license. Copy of the license.
• Makefile
  Makefile to build geneid binary.
• README
  This file contains information about how to install and run the program, and other more recent information.

Compiling geneid code

Enter the geneid directory and then, to build the binary file use the make tool:

- cd geneid
- make

The binary geneid will have been created into the bin directory. Type diff bin/geneid -h to test the file has been properly built.

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Enrique Blanco Garcia © 2003