/cgpPindel

Cancer Genome Project Insertion/Deletion detection pipeline based around Pindel

Primary LanguagePerlGNU Affero General Public License v3.0AGPL-3.0

cgpPindel

cgpPindel contains the Cancer Genome Projects workflow for pindel.

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The is a lightly modified version of pindel v2.0 with CGP specific processing for:

  • Input file generation
  • Conversion from pindel text output to:
    • tumour and normal BAM alignment files
    • VCF
    • Application of VCF filters.

###Dependencies/Install

Please install the following first:

Please see these for any child dependencies.

Once complete please run:

./setup.sh /some/install/location

Please use setup.sh to install any other dependencies. Setting the environment variable CGP_PERLLIBS allows you to to append to PERL5LIB during install. Without this all dependancies are installed into the target area.

Please be aware that this expects basic C compilation libraries and tools to be available.

##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 perl/lib/Sanger/CGP/Pindel.pm to the correct version (adding rc/beta to end if applicable).
  2. Update CHANGES.md to show major items.
  3. Run ./prerelease.sh
  4. Check all tests and coverage reports are acceptable.
  5. Commit the updated docs and updated module/version.
  6. Push commits.
  7. Use the GitHub tools to draft a release.

LICENCE

Copyright (c) 2014-2016 Genome Research Ltd.

Author: Cancer Genome Project cgpit@sanger.ac.uk

This file is part of cgpPindel.

cgpPindel is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see http://www.gnu.org/licenses/.

  1. The usage of a range of years within a copyright statement contained within this distribution should be interpreted as being equivalent to a list of years including the first and last year specified and all consecutive years between them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- 2009, 2011-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, 2009, 2010, 2011, 2012’."