PSORTb version 3.0.0 Installation Instructions

OVERVIEW

The manual script for the new version of PSORTb (v.3.0) is in preparation. In the mean time, please cite this publication if you use PSORTb in your research:

Gardy, J.L., Laird, M.R., Chen, F., Rey, S., Walsh, C.J., Ester, M., Brinkman, F.S. PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21(5):617-23.

The standalone version of PSORTb is distributed under the GNU General Public Licence (Gnu GPL). The program was initially developed for the Linux environment, but has since been ported to OS X (Darwin). It will NOT run correctly on any OS X version newer than 10.4.

This document describes the installation of the PSORTb version 3.0 command line program and the PSORTb server packages. For most purposes, following the installation instructions for the command line version will be sufficient - the server package installation instructions are only necessary if one wishes to set up their own local PSORTb server.

For further information, please contact psort-mail@sfu.ca.


PREREQUISITES

PSORTb has several prerequisites that must be installed for a fully functional version.

1. Either a Linux distribution or Mac OS X
PSORTb has been tested and found to work on the following Linux distributions to date: Ubuntu, SuSE, Red Hat, Debian, Mac OS X 10.4 (NOT newer versions).

2. Perl version 5.005_03 or higher (5.6.x or higher recommended)
The latest version of Perl can be obtained from http://www.cpan.org

3. The Bioperl library version 1.2.x or higher
While PSORTb *has* been tested on earlier versions of Bioperl, the latest version is strongly recommended. Bioperl can be obtained from http://www.bioperl.org

IMPORTANT NOTE REGARDING BIOPERL: There seems to be a problem between Bioperl and BLAST on some platforms, in which the system call to BLAST returns a -1 return code. Unfortunately, despite our best efforts, we have not been able to solve this problem. As a result, PSORTb may not run properly when installed onto certain platforms. This problem has been reported on a small number of machines to date running PSORTb under RedHat 9.0 and Solaris. The problem is not apparent, however, on other machines running these distributions, or when the program was tested under RedHat 7.3, SuSE 9.0, and Mandrake 9.2.

If you encounter this problem, we have developed a workaround. Comment out the line:

$self->throw("$executable call crashed: $? $commandstring\n")unless ($status==0) ;

in the file Bio/Tools/Run/StandAloneBlast.pm at approximately line 633.

Please contact us at psort-mail@sfu.ca in the event that you find this problem occuring under other distributions, or if the workaround does not solve the problem. Please include in your email your operating system type and version, the version of Perl you are using (the output of 'perl -V' is best), and the version of Bio::Tools::PSort you are using. Your feedback will help us in solving this problem!

4. A working installation of standalone NCBI BLAST
BLAST can be obtained from the NCBI FTP site at ftp://ftp.ncbi.nih.gov/blast/executables/

5. A working installation of PFTOOLS
PFTOOLS can be obtained from http://www.isrec.isb-sib.ch/ftp-server/pftools/pft2.3/
If you do not have a Fortran compiler, pre-compiled pftools executables are available for some of the commoning used operating systems. If you are unable to find a version for your operating system, it is still possible to install PSORTb, but note that Profile and Motif analyses will not be performed.


INSTALLATION

Please ensure that you have installed all of the prerequisite packages before performing this step.

libpsortb-1.0 has been tested under linux/x86, linux/x86_64, OSX Other operating systems are not supported at this time, but it doesn't mean the package won't work. Testing has been a matter of access to different OS and hardware platforms. If you have success with another platform, or would like our assistance porting the package to your platform please contact us. Installation should be as simple as:

./configure
make
make install
ldconfig

configure takes the usual parameters, however the final libraries must be in a path that the dynamic linker from Perl can find.

Unzip the Bio-Tools-PSort archive. Next, in the directory created when you unzipped the Bio-Tools-PSort archive, run the following commands (Note that you will most likely have to have administrative privileges to run these commands successfully):

perl Makefile.PL
make
make test
(optional, but recommended)
make install

This should install and test all of the modules distributed with the package. If this step is successful, please proceed to the next step - configuring standalone PSORTb.


CONFIGURING STANDALONE PSORTb

Bio::Tools::PSort stores per-module configurations and other necessary files under the 'psort' directory. These files are not installed in the previous step, and it is recommended that you copy this directory to a more permanent location like /usr/local/psort/ using a command like cp -r psort /usr/local/

This command will create a new directory called /usr/local/psort/. Note that you will have to have the appropriate permissions to execute this command.

It is also necessary to create the BLAST database used by the Bio::Tools::Run::SCLBlast module. After performing the above step, switch into the $PSORT_ROOT/conf/analysis/sclblast directory (where $PSORT_ROOT is the directory where you just copied the files to), and using the formatdb program distributed with the NCBI BLAST package, run the command (ensuring the formatdb is in your $PATH variable) makedb.sh

Standalone PSORTb requires several environment variables to be set so that it can find the locations of various programs it requires. You will have to set the following variables:

PSORT_ROOT
PSORT_PFTOOLS
BLASTDIR

to point to the PSORT_ROOT directory, the location of the HMMTOP installation directory, the location of PFTOOLS (pfscan specifically) and the location of the BLAST installation, respectively.

A local PSORTb program is available in $PSORT_ROOT/bin and can be used to test your setup.

Once this step has been successfully completed, installation of standalone PSORTb is complete. This will be sufficient for most users of the program.