kellrott / pcap-core

NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project

ICGC-TCGA-PCAP

NGS reference implementations and helper code for the ICGC/TCGA Pan-Cancer Analysis Project

This repository contains code to run genomic alignments of paired end data and subsequent calling algorithms.

The intention is to provide reference implementations and simple to execute wrappers that are useful for the scientific community who may have little IT/bioinformatic support.

Please see the wiki for further details.

---

###Dependencies/Install Some of the code included in this package has dependencies on several C packages:

• biobambam
• bwa
• samtools

And various perl modules.

Please use setup.sh to install the dependencies. Please be aware that this expects basic C compilation libraries and tools to be available, most are listed in INSTALL.

---

###Programs

Please see the wiki for details of programs.

---

##Creating a release ####Preparation

• Commit/push all relevant changes.
• Pull a clean version of the repo and use this for the following steps.

####Cutting the release

1. Update lib/PCAP.pm to the correct version (adding rc/beta to end if applicable).
2. Ensure upgrade path for new version number is added to lib/PCAP.pm.
3. Update Changes to show major items.
4. Run ./prerelease.sh
5. Check all tests and coverage reports are acceptable.
6. Commit the updated docs tree and updated module/version.
7. Push commits.
8. Use the GitHub tools to draft a release.