2metDB Files

README

The pipeline is a version of the version of the NRPS-PKS Analysis web-site that can be found at nrps.igs.umaryland.edu/nrps/
This version input an entire genome proteome (multifasta file) and scans each proteins for NRPS/PKS genes. The output is similar to that of the NRPS-PKS Analysis web-site.

Installation

Requirements 

    The following dependencies are necessary:
    
    1. Latest NCBI blast (can be downloaded at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/)
    
    2. HMMER from Sean Eddy (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/hmmer-2.3.2.bin.powerpc-apple-osx.tar.gz)
    These binaries need to be installed at /usr/local/bin/ . If they are not install at this location, the script 2metdb.pl will need to be modified. At line 33 and 34 change the following with the appropriate path of the executable. 
	33   my $HMMER_PATH = "/usr/local/bin";
	34   my $BLAST_PATH = "/usr/local/bin";

	Alternatively, a symlink can be placed at /usr/local/bin/ using the following command from inside /usr/local/bin (requires sudo privileges : sudo ln -s /path_to_blastall/blastall blastall and sudo ln -s /path_to_hmmpfam/hmmpfam hmmpfam  
    
    3. WEB SHARING
	Personal web_sharing needs to be enable in the System Preference/Sharing window.


Installing the scripts and dependencies. 

Download the .tar file HERE.
Copy the file to your Desktop, double click on it, it will uncompress and you should see a folder name 2metdb_genome_scan
open Terminal 
at the prompt type:
cd /Desktop/2metdb_genome_scan  then return
you are now inside the folder, type
install.sh   then return
You'll be prompted to enter your password. It has to be a password with admin privilege.

The install script is run and all the necessary files have been copied to the right place
Three folders /lib /database /hmm have been copied to /Library/WebServer/CGI-Executables/ along the main script 2metdb.pl
One folder /genome has been copied to /Library/WebServer/Documents/ 

How to run the script

The script is a command line script and generate an .html file that can be viewed inside your browser at the following location: http://localhost/genome/filename.html

To run the script

Open Terminal
at the prompt type:
cd /Library/WebServer/CGI-Executables/
2metdb.pl path_to_multifasta_peptide_file > ../Documents/genome/filename.html

where path_to_multifasta_peptide_file is the path of the input file, a genome proteome in multifasta format.
and filename.html is a filename you want to give to the output.

Once the script has run, you can view the output at http://localhost/genome/filename.html
The output is similar to the NRPS-PKS Analysis Website at http://www.tigr.org/jravel/nrps/ . Please visit the site for more information on how to read the output.