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 - currently available internally only 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.