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northeyt / TCNlib

A library of perl modules from my PhD, mostly for working with PDB structures
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About

This github is home to a bunch of perl modules and scripts that were written during the course of my PhD. Most modules are written using Moose, the perl library for object-orientation. The main bulk of the modules are used to manipulate PDB files and in particular to send or process data to and from bioptools programs.

Setup

These prerequisites are required for TCNlib

  1. Install bioptools, available via github.

  2. Install BioPerl. See the BioPerl website for instructions. I recommend opening the cpan client on the command line and typing d /bioperl/. This will return a list of available BioPerl packages. Pick the most recent version and use force to install (it is likely that some tests will fail) by running force install CJFIELDS/BioPerl-1.6.924.tar.gz.

  3. Install Module::Build, which is required to check for and install perl dependecies. Run cpan Module::Build on the command-line to install it.

  4. Run setup.pl. This installs git submodules and external packages, checks for perl dependencies (installing any that are missing) and makes a working copy of lib/TCNPerlVars.pm from lib/TCNPerlVars.defaults.

  5. Run tests using runtests.pl.

  6. Add the following lines to your .bashrc:

export TCNlib=/path/to/TCNlib
export PERL5LIB=$TCNlib/lib:$PERL5LIB

Where /path/to/TCNlib/ is replaced with the real path!

  1. Get swissprot for blast searches (not necessary, but recommended!). Running blast searches remotely is implemented in this library, but the NCBI cgi server can be unreliable and is always slow. To run blast searches against a local version of the swissprot database, run setup-blastdb. This will grab the latest version of swissprot from the NCBI FTP server and create the required database files so that blastall can be run. The files will be created at the location specified by the $TCNPerlVars::blastdbDir variable, found in TCNPerlVars.pm. Alternatively, if you already have a local version of the database, point the $TCNPerlVars::swissProtDB towards it.