Arlecore Readme

ARLECORE (v 3.5.
2)
==========
ARLECORE is the console version of Arlequin"
Usage:
-----arlecore <project file name (*.arp)> | <settings file (*.ars)>
| run_silent\n
The three arguments are optional. If no argument is provided
arlecore will look for the file arl_run.txt where the name of a
project file should be indicated. If it does not find the project
file defined in arl_run.txt, the present message is shown.
The argument <project file name> needs to be put within quotes if
it contains whitepaces
The argument <settings file (*.ars)> allows one to use
a specific setting file for the computations.
If no settings file is specified, it will use the default setting file
arl_run.ars.
run_silent: if present on the command line, arlecore will not output
computation progress in the console
Examples:
arlecore test.arp test.ars
This will analyse the file 'test.arp' using the settings defined in the
file 'test.ars'.
arlecore
This will read the file 'arl_run.txt' to see which project(s) need(s) to
be analysed, and which setting file to use (arl_run.ars) or <project name>.
ars.
What is needed to run arlecore:
------------------------------ arlecore executable file under windows or linux
- a settings file (e.g. arl_run.ars) created with the windows version of arlequi
n (see below)
What is needed to properly view the html or xml result files:
- All the gif, js, xsl, and R files provided in the archive file arlecore*.zip
Different flavors of arlecore:

-----------------------------We provide these different versions of arlecore:
- arlecore64.exe
: 64 bit windows executable
- arlecore32.exe
: 32 bit windows executable
- arlecore352_64bit : 64 bit Linux version
- arlecoremac_64bit : 64 bit MacOS version
How to set up the setting file arl_run.ars:
------------------------------------------- Launch the Windows version or Arlequin
- Open a project file of the type you want to analyse

- Choose the computations you want to perform in the settings tab
- Press on the Save button above the Arlequin settings pane. Choose a place and
a
name (arl_run.ars is the default name) for the settings you have just selected
.
- If you close the project without explicitly saving your settings, they will be
saved by default in the file arl_run.ars.
These settings file contain all necessary information about which computations
to perform and which parameters to use for those computations.
- Copy this file in the directory of the arlecore executable file,
or else you will need to specify its full path when invoking arlecore (see abo
ve)
- Note that the same settings file can be used under both windows and linux.
Bash script to launch arlecore

-----------------------------We provide with arlecore a basic bash script called LaunchArlecore.sh,
allowing one to run arlecore on all the files present in a given directory.
It assumes that this directory also contains arlecore, as well as a setting file
.
This bash script will run on Linux by just typing the command
./LaunchArlecore.sh
and on windows by typing the command
bash LaunchArlecore.sh
assuming you have installed the cygwin package (available on http://www.cygwin.c
om/), or the
msys package (http://www.mingw.org/wiki/msys) and that the
cygwin/bin or MinGW\msys\1.0\bin directory is on your path environment variable.
Note that you'll need to edit LaunchArlecore.sh (with any text editor - not Word
) to specify:
- the version of arlecore you are using
- the name of the settings file you want to use
Bash script LaunchArecore.sh

------------------------------#!/bin/bash
#Laurent Excoffier November 2009
#
#The script will launch arlecore on all arlequin project files in turn
#It assumes that it is launched in a directory containing:
#
- a series of *.arp files to be analysed
#
- a settings file containing the settings specifying which
#
computations are to be performed (usually obtained through the Wi
nArl35.exe
#
graphical interface).
#Modify the following line to state which version of arlsumstat you are using
arlecore=arlecore35_64bit
#Modify this if you wan to use another setting file
settingsFile=arl_run.ars
if [ -f $settingsFile ]; then
#This loop will analyse all files with the same settings file
for file in *.arp
do
echo "Processing file $file"
#Launch arlecore with the same settings for all files
./$arlecore $file $settingsFile run_silent
done
#The following loop would be an alternative to perform specific computatio
ns on each file
#assuming that there is a different setting file with the same name as the
project file, but with
#the extension *.ars
#for file in *.arp
#do
# echo "Processing file $file"
# #Launch arlecore with project specific settings
# ./$arlecore $file ${file%.*}.ars run_silent
#done
else
echo "Settings file $settingsFile does not exist. Aborting script."
fi
Running a single instance of arlecore on the command line

----------------------------------------------------------Examples under windows:
The following command will analyse the file test.arp
using the default arl_run.ars setting file
./arlecore64.exe test.arp
The following command will analyse the file test.arp
using the setting file test.ars
./arlecore_32bit test.arp test.ars
be analysed, and which setting file to use (arl_run.ars) or <project name>.ars
./arlecore64.exe
be analysed, and the settings file test.ars will be used for these analyses
(assuming that files will be analyses using arlequin interface settings
i.e. keyword 'use_interf_settings' presnet on the 2nd line of arl_run.txt)
./arlecore64.exe test.ars
----Laurent Excoffier, April 2015
Email: [email protected]

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ARLECORE (v 3.5.

Different flavors of arlecore:

- Open a project file of the type you want to analyse

Bash script to launch arlecore

Bash script LaunchArecore.sh

Running a single instance of arlecore on the command line

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