Installation and requirements

This tutorial describes step by step how to install and run eFindSitePPI locally. If you have only a few targets, you can use the webserver. If you prefer to use it locally, please follow the installation procedures described below. Here, we will install eFindSitePPI in /usr/local/. Should you use a different location, please make the appropriate changes.

Perl modules

First, install the following Perl modules, which are available from CPAN:

File::Temp http://search.cpan.org/~dagolden/File-Temp-0.2301/
File::Slurp http://search.cpan.org/~uri/File-Slurp-9999.19/
File::Copy http://search.cpan.org/~rjbs/perl-5.18.1/
Compress::Zlib http://search.cpan.org/~pmqs/IO-Compress-2.063/
AI::NaiveBayes1 http://search.cpan.org/~vlado/AI-NaiveBayes1-2.006/
List::Util http://search.cpan.org/~pevans/Scalar-List-Utils-1.35/
Algorithm::NeedlemanWunsch http://search.cpan.org/~vbar/Algorithm-NeedlemanWunsch-0.04/
Benchmark http://search.cpan.org/~rjbs/perl-5.18.1/
Cwd http://search.cpan.org/~smueller/PathTools-3.40/
YAML http://search.cpan.org/~ingy/YAML-0.88/

For instructions on how to install Per modules, see http://www.cpan.org/modules/INSTALL.html.

Additional software

In order to use eFindSitePPI, you will need several additional programs. All these programs are free for academic and non-commercial users; however, some of them do require user registration and/or signing a license agreement. Before downloading and using them, please make sure that you comply with legal and other requirements; we are not responsible for illegal use of third-party software. Moreover, some of these codes are available for packet managers, such as yum (e.g. Red Hat), apt-get (e.g. Ubuntu) or MacPorts (Mac OSX). This is a recommended option and it will save you some time. Additional software is described in the tables below.

LIBSVM Support Vector Machines for classification and regression
NACCESS Atomic solvent accessible area calculations
fr-TM-align Protein structural alignment

Installation

Download the latest version of eFindSitePPI from here, unpack the tarball, go to efindsiteppi-1.0/src/ and run make:

[local]$ tar xzf efindsiteppi-1.0.tar.gz

[local]$ cd efindsiteppi-1.0/src/

[src]$ make

If there are no problems, the following files will show up in efindsiteppi-1.0/bin/:

[src]$ ls ../bin/

efindsiteppi
efindsiteppi_map

 

© Michal Brylinski
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