BioAfrica - GDE for Linux Installation Instructions:

GDE for Linux installation instructions:

1. Basics
2. Preparing the environment
3. Installing necessary bioinformatics software for running GDE for Linux
4. Installing GDE for Linux
5. Set the environment variable GDE_HELP_DIR to that location in your login/startup files.
6. Copy the GDE menus file (/usr/local/biotools/GDE/CORE/.GDEmenus) to each user home directory
7. Making scripts and database directories
8. (optional) Add local BLAST and sequence databases Scripts.
9. (optional) Adding Website links
10. Start GDE for Linux
11. First contact and basic navigation
12. Testing the software, Importing Sequence
13. I expect that the tutorials movies in quick time in how to use GDE for sequence analysis can be very useful. A simple text tutorial is also available
14. Questions, suggestions and contributions

1. Basics:
The GDE linux distribution had been compiled for a GNU/Linux system, until today GDE for linux had been successful setup in Debian, RedHat, Mandrake and FreeBSD Linux distributions. You must have installed the PERL interpreter (recommended version 5.005 or superior, the programs project that interpreter PERL are assumed to be in the /usr/bin/perl directory). It is also necessary to have the sed installed (we use the GNU sed version 3.02).
To check if your system have the PERL and sed packages.

[your_host] $ whereis perl
[your_host] $ whereis sed

2. Preparing the environment.
Before running the GDE for Linux you must install the XView libraries. Please download your packages distribution. If you use Debian GNU/Linux you can install the xviewg_3.2p1.4-9.deb and xviewg-dev_3.2p1.4-9.deb, that are localized in the software download section. If you use the RedHat or Mandrake GNU/Linux download the .rpm files. For others GNU/Linux distributions download the tar.gz files and compile t hen.

Debian:
[your_host] $ dpkg -i xviewg_3.2p1.4-9.deb
[your_host] $ dpkg -i xviewg-dev_3.2p1.4-9.deb

RedHat:
[your_host] $ rpm -i xview-3.2p1.4-6.i386.rpm
[your_host] $ rpm -i xview-clients-3.2p1.4-6.i386.rpm

Other Linux distribution:
[your_host] $ tar -zxvf xview_3.2p1.4.tar.gz
[your_host] $ imake

3. Installing necessary bioinformatics software for running GDE for Linux:
Others programs are necessary for using GDE for Linux, and can be download here.

NCBI tools and local blast searches.

Clustalw, alignment tool.

Readseq, sequence convertor format.

Phylip, phylogenetic analysis

Treetool, phylogenetic tree visualize

Attention: If you do not use Debian, RedHat, or Mandrake GNU/Linux distribution, download the tar.gz files and compile them.

4. Installing GDE for Linux
Copy the file GDElinux.tar.gz to the desired directory. ( I suggest you to install GDE for linux in the /usr/local/biotools/GDE . GDE menu files are pre-configurate to look for bioinformatics tools and databases at /usr/loca/biotools/ and /usr/local/biotools/db.)

[your_host] $ mkdir /usr/local/biotools
[your_host] $ cp GDElinux.tar.gz /usr/local/biotools
[your_host] $ tar -zxvf GDElinux.tar.gz

5. Set the environment variable GDE_HELP_DIR to that location in your login/startup files.

Mine uses bash:
[your_host] $ export GDE_HELP_DIR=/usr/local/biotools/GDE/CORE

tcsh:
[your_host] $ setenv GDE_HELP_DIR /usr/local/biotools/GDE/CORE

Set the environment variable in the .bash_profile (for bash) and .tcsh (for tcsh) files at your home directory.

6. Copy the GDE menus file (/usr/local/biotools/GDE/CORE/.GDEmenus) to each user home directory.
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This file (.GDEmenus) will create the menus in GDE and can be easily configured easily to adapt to researcher interests and needing.
This file (.GDEmenus) when located in your home directory will control the GDE menu appearance, and it this file that you will need to modify to add specific databases, sequence datasets and novel bioinformatics software.
The tutorial explain how to setup new software and datasets in .GDEmenus.

7. Making scripts and database directories.

Make the following directories in your home directory:
[your_host] $ mkdir GDE/
[your_host] $ mkdir GDE/bin # directory for scripts for blast and dataset setup
[your_host] $ mkdir GDE/db # directory for local sequence database database)

8. (optional) Add local BLAST and sequence databases Scripts.

8.1 Copy the blast (/usr/local/biotools/GDE/installBLASTDBDNA.pl, and /usr/local/biotools/GDE/installBLASTDBPROT.pl), and dataset (/usr/local/biotools/GDE/newDATASET.pl) PERL scripts to home GDE/bin/ directory.

[your_host] $ cp /usr/local/biotools/GDE/installBLASTDBDNA.pl /your_home/GDE/bin/
[your_host] $ cp /usr/local/biotools/GDE/newDATASET.pl /your_home/GDE/bin/

Edit the scripts (installBLASTDBDNA.pl, installBLASTDBPROT.pl and newDATASET.pl) and setup the correct home and database variables:
$DB= "/your_home/GDE/db"
$HOME= "/your_home/"

8.2 Set the environment variable DATABASE and SCRIPTS to GDE/db/ and GDE/scripts directories

Mine uses bash:
[your_host] $ export DATABASE=/your_home/GDE/db/
[your_host] $ export SCRIPTS=/your_home/GDE/scripts/

tcsh:
[your_host] $ setenv DATABASE /your_home/GDE/db/
[your_host] $ setenv SCRIPTS /your_home/GDE/scripts/

Set the environment variable in the .bash_profile (for bash) and .tcsh (for tcsh) files at your home directory.

9. (optional) Adding Website links.

Copy the newURL PERL script to GDE/bin/ directory.
[your_host] $ cp /usr/local/biotools/GDE/bin/newURL.pl /your_home/GDE/bin/

Edit the script newURL.pl and setup the correct home variable
$HOME= "/your_home/"

10. Start GDE for Linux
GDE executable is found at /usr/local/biotools/GDE/bin/gde

Start the program:
[your_host] $ /usr/local/biotools/GDE/bin/gde

Note: You can set the GDE executable file in the PATH variable in the .bash_profile (for bash) and .tcsh (for tcsh) files at your home directory or
Link the executable to the bin directory (need root privileges)
[your_host]$ ln -s /usr/local/biotools/GDE/bin/gde /bin/gde)

11. First contact and basic navigation.

The genetic data environment (GDE) is a graphical view for manipulating DNA and amino acid sequences. Sequences can be edited and analyzed by many others bioinformatics software in your system. Please read the documentation to learn how to perform basic sequence analysis.

The menu entries are viewed by mouse right click over the menu, and executed by mouse left click.

12. Testing the software, Importing Sequence.

Copy the test.fasta file to your home directory.
[your_host] $ cp /usr/local/biotools/GDE/test.fasta ./

In the GDE interface, right_click in the File Menu, and choose the Import function (left_click)
Type the file name: test.fasta
Press OK.

If the sequences appears in the GDE interface, you had correct followed all the steps and your system in ready to run the GDE for Linux.
Congratulations !!!

*** NOTE: If GDE for Linux could not be started, please refer to the Questions & Answers section (troubleshooting)

13. I expect that the tutorials movies in quick time in how to use GDE for sequence analysis can be very useful. A simple text tutorial is also available.

Documentation available:

Installation instruction.

Questions and Answers (Troubleshooting).

GDE for Linux basic functions tutorial (alignment, translation, phylogenetic tree construction, etc.)

How to cite GDE for Linux in a publication.

How to integrate bioinformatics software editing the menu file (.GDEmenus) [PDF file]

GDE documentation and tutorials online.

14. Questions, suggestions and contributions:
The Bioafrica network web site contain a lot of resources for GDE for linux. Including bioinformatics software integrated in GDE , specific microbial sequence datasets integrated with GDE for linux and online resources for sequence analysis.

Adding new functions to GDE for Linux is fun and easy, please send me menus that had been created for others bioinformatics software, also we are an active community and fell free to send questions and suggestions to:

The BioAfrica web site is maintained by: Dr. Tulio de Oliveira,