https://github.com/icgc-tcga-pancancer/pcap-core

Legacy, see cancerit/PCAP-core: NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project
https://github.com/icgc-tcga-pancancer/pcap-core

icgc legacy-support pcap perl

Last synced: 3 months ago
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Legacy, see cancerit/PCAP-core: NGS reference implementations and helper code for the IGCG/TCGA Pan-Cancer Analysis Project

• Host: GitHub
• URL: https://github.com/icgc-tcga-pancancer/pcap-core
• Owner: ICGC-TCGA-PanCancer
• License: gpl-2.0
• Created: 2014-02-04T22:06:24.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2024-06-12T23:30:32.000Z (5 months ago)
• Last Synced: 2024-07-16T11:01:48.069Z (4 months ago)
• Topics: icgc, legacy-support, pcap, perl
• Language: Perl
• Homepage:
• Size: 14.6 MB
• Stars: 13
• Watchers: 8
• Forks: 14
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGES.md
  • License: LICENSE

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README

        
ICGC-TCGA-PCAP

==============

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

| Master | Dev |

|---|---|

| [![Build Status](https://travis-ci.org/ICGC-TCGA-PanCancer/PCAP-core.svg?branch=master)](https://travis-ci.org/ICGC-TCGA-PanCancer/PCAP-core) |  [![Build Status](https://travis-ci.org/ICGC-TCGA-PanCancer/PCAP-core.svg?branch=dev)](https://travis-ci.org/ICGC-TCGA-PanCancer/PCAP-core) |

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](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/wiki) for further details.

---

###Dependencies/Install

Please install the following before running `setup.sh`:

* [cgpBigWig](https://github.com/cancerit/cgpBigWig/releases)

* Addtional OS packages required by `kentsrc`, in Ubuntu naming

  * unzip

  * libpng12-dev (for libpng-config)

Dependancies installed by `setup.sh`:

* [biobambam](https://github.com/gt1/biobambam)

* [bwa](https://github.com/lh3/bwa)

* [samtools](https://github.com/samtools/samtools)

And various perl modules.

Please see the respective licence for each before use.

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](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/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.

2. Ensure upgrade path for new version number is added to `lib/PCAP.pm`.

3. Update `CHANGES.md` 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.