geneid documentation: 3. How to install geneid

Table of contents:

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:

  1. Type gzip -d geneid.tar.gz
  2. Type tar -xvf geneid.tar
Under Linux, try:
  1. Type 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.
  • src/
    geneid source code.
  • GNULicense
    This software has been registered under this license. Copy of the license.
  • Makefile
    Makefile to build geneid binary.
    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:
  1. Type cd geneid
  2. Type make
The binary geneid will have been created into the bin directory. Type bin/geneid -h to test the file has been properly built.

Enrique Blanco Garcia © 2001