README

WTSI NPG useful_modules package
-------------------------------

General purpose scripts and modules used by WTSI Illumina sequencing production pipeline and manual data processing.

Dependencies on other NPG Perl packages:

1. npg_tracking package https://github.com/wtsi-npg/npg_tracking
2. npg-qc package - https://github.com/wtsi-npg/npg_qc

Dependencies on other NPG bioinformatics tools

1. illumina2bam https://github.com/wtsi-npg/illumina2bam
2. samtools_irods https://github.com/wtsi-npg/samtools_irods

Dependencies on third party bioinformatics tools

1. bwa http://bio-bwa.sourceforge.net/
2. samtools http://samtools.sourceforge.net/
3. picard http://picard.sourceforge.net/
4. cram toolkit https://github.com/jkbonfield/samtools.git
5. biobambam https://github.com/gt1/biobambam

Installation:

perl Build.PL --install_base your_dir
./Build
./Build installdeps --cpan_client 'cpan -i' #to install cpan dependencies, ensure cpan was built with the perl you are using for this build
./Build test
./Build install

Tests where real bioinformatics tools are used are skipped by default. Set TOOLS_INSTALLED environment variable to true to run these tests. It is expected that third party executables are found on the path. Java jar files are expected to be found in a directory pointed by the CLASSPATH envronment variable.