INSTALLATION INSTRUCTIONS FOR prot4EST version 1.0

CONTENTS

1. Installing prot4EST
2. Getting External Dependencies - important information on a bug in ESTScan and the fix provided.
3. Environmental Variables


1. Installing prot4EST

prot4EST can be obtained from our website (http://www.nematodes.org/PartiGene).  

If you wish to be kept up to date with version releases and other news relating to our software then please enter your email address into the box provided.  
Your address will not be passed on to anyone else.

Follow the 'downloads' link to a list of programs.  

i - Click on prot4EST_XXX.tar.gz to save the latest version.  Where xxx is 
the version number.

ii- Unzip and unpack the tarball:

#> gunzip prot4EST_XXX.tar.gz
#> tar -xvf prot4EST_XXX.tar

This will unpackage the contents into the directory prot4EST_xxx/.  

#> cd prot4EST_xxx

The directory should contain the following files:

config.example - example of the config file used to launch prot4EST (see below).
prot4EST_UG.pdf - a copy of this user guide.
seq_files/mito.fsa - protein sequences from mitochondria encoded genes (obtained from GenBank).
seq_files/rRNA.fsa - nucleotide sequences for ribosomal RNA genes (obtained from GenBank).
scripts/prot4EST.pl - the main Perl script.

Makefile.PL - the installation script

iii - To install the program use the following commands:
#> ./Makefile.PL
#> make
log in as root
#> su
#> make install

If the install is successful then the main program prot4EST is in '/usr/bin/' and all the required scripts have been moved into 
your Perl path.

iv. Additional Files
There are three files that contain BLAST databases:
mito_metaNfungi.bldb.tar.gz - Metazoan and Fungal mitochondrially-encoded proteins
mito_viridiplantae.bldb.tar.gz - Viridiplantae mitochondrially-encoded proteins
rRNA.bls.tar.gz - ribosomal RNA sequences
To unpack these:
#>tar -zxvf file.tar.gz
You can place these anywhere, but I recommend they are moved to the directory containing other blast databases, e.g. 
/usr/local/ncbi/db

gc.prt contains the genetic codes. Again the location of this file is up to you.

2. Getting Dependencies
prot4EST is a  pipeline  program: it takes an input file and processes it through a series of steps to give an output. Some of 
these steps are built in to prot4EST, while others rely on using external programs. Detailed below is a list of programs that 
need to be installed for the successful running of prot4EST.  Where a license is required, all free to academic users, details 
are provided.
                                                                                                                                                                                        
Perl (http://www.perl.org)
BioPerl version 1.4 (http://www.bioperl.org)
EMBOSS (http://www.emboss.org)
NCBI BLAST - standalone package (ftp://ftp.ncbi.nih.gov/blast/executables/LATEST)
ESTScan_v2.0 - distributed under GNU license (http://www.isrec.isb-sib.ch/ftp-server/ESTScan/)
DECODER - license free for accademic use; email genome.ofc-@gsc;riken.jp
ANSIColor.pm (http://www.cpan.org) - may already be installed, type locate ANSIcolor.pm to check.
                                                                                                                                                                                        
Installing all of these packages is simple and the distributions of these programs provide full details.  To realise the full 
potential of prot4EST, it is important that both ESTScan and DECODER are installed.

NOTE:
There is a bug in ESTScan which may cause prot4EST to crash. It is relatively simple to correct and to make the experience even more enjoyable I have included a script that will amend the problem.
To run it make sure you're in the prot4EST_X.X.X directory and type: './fix_estscan.pl' .

                                                                                                                                                                                        
3. Environmental Variables
To help the smooth running of prot4EST it is necessary to set up certain environmental variables.  These are outlined in the 
installation instructions for the respective programs.  These include BLASTMAT and BLASTDB for NCBI BLAST.  It is also 
beneficial to put the environmental variable ESTSCANDIR in the initialisation file (.bashrc / .cshrc).  This variable contains 
the directory path for ESTScan once you have installed it (e.g. setenv ESTSCANDIR /usr/local/ESTScan).  The exact location and 
format required to set up environmental variables is dependent upon the shell used on your Linux operating system.

4. Finally
I welcome any questions, suggestions or offers of PostDoc positions. Please email me at nematode.bioinf@ed.ac.uk
