This repository contains the internally-developed software used by the
Vertebrate Resequencing group a the Sanger Institute.

It comprises mostly self-documented Perl code. There are both scripts and 
modules within subfolders.

Each module has its own POD, so please use perldoc or similar for further help.
Eg:
$ perldoc VertRes::Utils::Sam

An overview, guides and how-tos are available on the github wiki:
https://github.com/VertebrateResequencing/vr-codebase/wiki



INSTALLATION
------------

You will need the source version of samtools compiled with -fPIC and -m64 in the
CFLAGS, and the environment variable SAMTOOLs pointing to that source directory
(which should now contain bam.h and libbam.a).
It is also recommended that you set PERL_INLINE_DIRECTORY to ~/.Inline


$ perl Build.PL

If this says you have "ERRORS/WARNINGS FOUND IN PREREQUISITES" try:
$ ./Build installdeps
to install missing prerequisites from CPAN.

To test the code prior to use:

$ perl Build.PL
$ ./Build test

To install:
$ ./Build install
(or just point your PERL5LIB to the modules subdirectory, and include the
scripts subdirectory in your PATH)


EXTERNAL SOFTWARE
-----------------

Most likely some of the tests will fail due to you not having certain external
software installed. If you don't plan on making use of that software, just
ignore it when a test script for that software fails. Some software also need
environment variables setup (using setenv in csh or export in bash). The
following list shows the name of the software, the environment variable you need
to set, and the value you should set it to, separated by commas.

samtools,SAMTOOLS,/path/to/samtools/source_directory
GATK,GATK,/path/to/gatk_jar_files
GATK,STING_DIR,/path/to/gatk_source_code_checkout
GATK,GATK_RESOURCES,/path/to/resource_files_like_reference_etc
picard,PICARD,/path/to/picard_jar_files
beagle,BEAGLE,/path/to/beagle_install_directory

eg. to have picard work properly in our pipelines you might do:
setenv PICARD /path/to/picard_jar_files
or
export PICARD=/path/to/picard_jar_files
depending on what shell you are using.


VRTRACK DATABASE
----------------

Tracking of meta-data, required for many of our pipelines, occurs in a mysql
database. We use more environement variables to define how to access the mysql
database:

VRTRACK_HOST
VRTRACK_PORT
VRTRACK_RO_USER
VRTRACK_RW_USER
VRTRACK_PASSWORD

The RW user you setup should have permissions to create and alter databases. We
assume that the RO user does not require a password.