Installation:
ANDES is
composed of a set of Perl and R scripts.
For aligning profiles, ANDES depends on clustalw2.
Perl
There is
an excellent chance that your release of Unix already has Perl installed. You can confirm this by typing the following at
the command line:
which
perl
You
should see a result that tells you the exact path of the perl binary that will
be executed by default, for example:
/usr/bin/perl
If you
get something like:
perl:
Command not found.
Then you
will need to either download perl yourself, or ask your system administrator
for help. Since this will be uncommon problem, we will not spend more time on
this.
Currently,
ANDES also uses the package Math::CDF.
http://search.cpan.org/CPAN/authors/id/C/CA/CALLAHAN/Math-CDF-0.1.tar.gz
To
install, please follow the instructions that are included. If you can, try to have the system administrator
install it in a central location so you will not have to deal with PERL5LIB
paths, and the like.
R
It is
more likely that you do not have R installed.
Fortunately, R is a very popular and well-maintained statistical
software package which is very easy to install.
To download R, go to the R website:
It is
easy to find the download link on their page; however, to initiate the
download, you will need to select the CRAN (Comprehensive R Archive Network)
mirror that is closest to you.
After
installation, if your shell is able to detect where Rscript is installed when
your invoke the following:
which Rscript
Then you
should already to go. If your shell
can’t find it, you may need to include the location of the Rscript binary in
your PATH environmental variable. How to
do this will vary depending on your shell.
Clustalw2
It is
also likely you may not have clustalw2 installed. You can download a copy from EBI at:
ftp://ftp.ebi.ac.uk/pub/software/clustalw2/
Follow
the installation instructions that they have provided. Chances are you just need to uncompress the
tar.gz file that you download and then make sure your PATH environmental
variable is pointed to where you uncompressed the tar file. Again you can test to see if your shell can
find clustalw2 by using the following command:
which clustalw2
ANDES
To
install ANDES, first go to our project download page, for the latest
version. You can find this at:
https://sourceforge.net/projects/andestools
Move the
archive to the directory you want to install ANDES, and then in that directory,
run the following command to uncompress and explode the archive.
tar -xvf ANDES_<release date>.tgz
The <release date> should contain the
date we uploaded the ANDES package, for example, 20091120. When you execute the tar command, the ANDES
directory will be created and all the Perl and R scripts, along with some
sample data will be created.
You’re
done.