cgpCaVEManWrapper

cgpCaVEManWrapper provides a simplified usage implementation for the complete Cancer Genome Project processing flow of the algorithm CaVEMan.

For details of the underlying algorithm please see the CaVEMan site.

For details of the filtering process please see the cgpCaVEManPostProcessing site.

Master	Develop

Docker, Singularity and Dockstore

There are pre-built images containing this codebase on quay.io.

• dockstore-cgpwxs
  • Contains tools specific to WXS analysis.
• dockstore-cgpwgs
  • Contains additional tools for WGS analysis.

These were primarily designed for use with dockstore.org but can be used as normal containers.

The docker images are know to work correctly after import into a singularity image.

Dependencies/Install

Please install the following first:

• linasm
• PCAP-core
• cgpCaVEManPostProcessing

Please see these for any child dependencies.

Once complete please run:

./setup.sh /some/install/location

This will automatically get the appropriate version of the core CaVEMan algorithm.

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/Caveman.pm to the correct version.
2. Run ./prerelease.sh
3. Check all tests and coverage reports are acceptable.
4. Commit the updated docs tree and updated module/version.
5. Push commits.
6. Use the GitHub tools to draft a release.

LICENCE

Copyright (c) 2014-2018 Genome Research Ltd.

Author: CASM/Cancer IT <cgphelp@sanger.ac.uk>

This file is part of cgpCaVEManWrapper.

cgpCaVEManWrapper 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
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