cancerit / dockstore-cgpbigwig

RETIRED: Dockstore implementation of cgpBigWig utility. See https://github.com/cancerit/cgpBigWig/

dockstore-cgpbigwig

dockstore-cgpbigwig Has been retired.

All components can now be found in the cgpBigWig

dockstore-cgpbigwig provides a suite of commandline tools written in C to manupulate BigWig files. These has been packaged specifically for use with the Dockstore.org framework.

Master	Develop

Supported Tools

Tools available in cgpBigWig supported in this docker:

• bwcat - Read the contents of a bigwig (.bw) file
• bam2bw - Generate bigwig (.bw) coverage file from bam
• bam2bedgraph - Generate a coverage bedgraph from bam
• bg2bw - Generate bigwig (.bw) coverage file from bedgraph (.bed) format
• bam2bwbases - Generate bigwig (.bw) proportion file of each base at a position from bam
• bwjoin - Concatenate bigwig files together

Test Data

The examples/ directory contains test data in .json files that can be used to verify the tools available.

Example reference files

In order to use the test examples for bam2bw, bam2bwbases, bg2bw, bwjoin reference information for Human GRCh37d5 is required. This can be downloaded and unpacked from our ftp site here. The reference paths in the .json example file should be updated to the location you have unpacked

wget ftp://ftp.sanger.ac.uk/pub/cancer/dockstore/human/core_ref_GRCh37d5.tar.gz

mkdir GRCh37d5

tar -C GRCh37d5 --strip 1 -zxf core_ref_GRCh37d5.tar.gz

Release process

This project is maintained using HubFlow.

1. Make appropriate changes
2. Bump version in Dockerfile and Dockstore.cwl
3. Push changes
4. Check state on Travis
5. Generate the release (add notes to GitHub)
6. Confirm that image has been built on quay.io
7. Update the dockstore entry, see their docs.

LICENCE

Copyright (c) 2016-2019 Genome Research Ltd.

Author: Cancer, Ageing and Somatic Mutation <[e-mail]>

This file is part of dockstore-cgpbigwig.

dockstore-cgpbigwig 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’."