Instructions for installing the Linux/Intel version of Arlequin 2.000

1. Archive file description

arlequin20_jre.tar	A self-extracting archive containing the two files below
arlequin20.tar.gz	A self-extracting archive containing all files necessary for running Arlequin
jre_glibc.tar.gz	Setup file for installing the Java Runtime Environment (ver. 1.1.7.) Only required if you have no Java Runtime Environment (ver. 1.1.7 or higher) already installed on your system

2. Software installation.

Depending on which of the three files you did download, follow the procedures described below

• If you have downloaded the complete package arlequin20_jre.tar, proceed as follows

Uncompress the archive with the command
tar -xvf arlequin20_jre.tar 
to obtain the two archive files arlequin20.tar.gz and jre_glibc.gz.  
To install the Java Runtime Environment and Arlequin, proceed as described below in the next two steps.

• Installation of the Java Runtime Environment from jre_glibc.tar.gz  

1. If you have the Red Hat 6 Linux version, download the jre_glibc.tar.gz file, otherwise go to Blackdown's home page for other ports and more documentation.
2. Copy the file jre_glibc.tar.gz or its equivalent into the directory /usr/local.
3. Decompress the archive with the command :
   tar -xvzf jre_glibc.tar.gz.
4. A directory jre_117_v3 containing all the necessary files will be created.
5. In the file ".bshcr" (initialization of the bash shell) add the following line:
   export PATH=/usr/local/jre_117_v3/bin:$PATH
   so that the shell knows where the jre file is.

• Installation of Arlequin from arlequin20.tar.gz 

1. After downloading the compressed file arlequin20.tar.gz from our web site, decompress it with the command
   gunzip arlequin20.tar.gz
   Then, Untar it with the command
   tar -xvf arlequin20.tar
   You can also do it in one step with the single command 
   ar -xvzf arlequin20.tar.gz
   
2. A directory called ArlequinFolder will be created, containing the file Arlequin.jar, the executable version of Arlequin 2.000 and all the necessary files to make the software run properly. Move this folder at any location of your hard disk. NOTE THAT ONCE YOU HAVE CHOSEN A LOCATION FOR THE SOFTWARE, YOU SHOULD NOT CHANGE IT, or it would become impossible to correctly browse the result files
   
3. To start Arlequin 2.000, double-click on the file called arlequin.bat. If it does not work, try either to launch arlequin.bat from a shell to see any error message. Altrnatively, try to type the following command in a shell:
   jre -cp arlequin.jar -cp swingall.jar arlequin.ArlequinApp
   

Arlequin Development Team
March 2000