Installation and requirements

Note: Here, we will install everything in /usr/local, if you want to use a different location, make the appropriate changes.

Required libraries

eVolver requires GNU Scientific Library, GSL, which can be downloaded from here: http://www.gnu.org/s/gsl/

You can install it from sources or using a packet manager, such as yum (e.g. Red Hat), apt-get (e.g. Ubuntu) or MacPorts (Mac OSX). If you installed GSL from sources, make sure it is recognized by your C++ compiler.

Additional software

To construct structure-based profiles, you need a structure alignment program. We recommend fr-TM-align, although other programs can also be used. If you plan on using a different structure alignment algorithm, you will likely have to write a simple script to convert generated alignments to a FASTA-like format that is recognized by eVolver; this is explained in the provided example.

For fr-TM-align, download it from http://cssb.biology.gatech.edu/fr-tm-align and follow the installation instructions.

You also need STRIDE to assign secondary structure. It can be downloaded from http://webclu.bio.wzw.tum.de/stride/. Again, follow the attached installation instructions (or see here).

Make sure that both external programs are available from the default search path:

[local]$ which frtmalign stride

/usr/local/bin/frtmalign
/usr/local/bin/stride

Of course, /usr/local/bin may be different on your system.

Perl modules

Next, install the following Perl module, which is available from CPAN:

File::Slurp http://search.cpan.org/~uri/File-Slurp-9999.19/

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

Compilation

Download the latest version of eVolver from our website (http://brylinski.cct.lsu.edu/content/evolver-standalone-package), unpack the tarball, go to evolver-1.0/src/ and run make:

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

[src]$ cd evolver-1.0/src/

[src]$ make

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

[src]$ ls ../bin/

eprofile
evolver

Structure library

Finally, you need a structure library, which can be downloaded from our website (http://brylinski.cct.lsu.edu/content/evolver-standalone-package). Unpack it to a convenient location, e.g. /usr/local/libraries/:

[local]$ mkdir libraries

[local]$ tar xzf evolver-lib-jan2012.tar.gz -C libraries/

 

© Michal Brylinski
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