CASM-Smart-Phase

| Master | Develop | | --------------------------------------------- | ----------------------------------------------- | | | |

• Container
• Smart-Phase
  • Running Smart-Phase
• Python utility scripts
• Docker image
• LICENCE

Container

This code is available as a docker image here quay.io/repository/wtsicgp/casm-smart-phase

Smart-Phase

The docker image also contains Smart-Phase

Please note, we do not support the Smart-Phase software, please contact the Smart-Phase repository owner.

Running Smart-Phase

In order to run smart-phase in the docker image either use the command:

```bash docker run quay.io/repository/wtsicgp/casm-smart-phase: java -jar /opt/wsi-t78/smartPhase.jar

usage: Welcome to SmartPhase! A dedicated tool designed to assist in the rapid and accurate phasing of variant combinations for clinical analysis. Please refer to the following list of options on how to pass the necessary parameters for use: .... ```

Python utility scripts

The python subdirectory contains utility scripts to merge Smart-Phase MNVs For more detail see the section README.

Docker image

Eventually this base directory will contain the Docker script for a Smart-Phase and utility script container.

LICENCE

```txt Copyright (c) 2021 Genome Research Ltd.

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

This file is part of CASM-Smart-Phase.

This program 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’." ```