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This code is available as a docker image here quay.io/repository/wtsicgp/casm-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.
In order to run smart-phase in the docker image either use the command:
docker run quay.io/repository/wtsicgp/casm-smart-phase:<version> 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:
....The python subdirectory contains utility scripts to merge Smart-Phase MNVs For more detail see the section README.
Eventually this base directory will contain the Docker script for a Smart-Phase and utility script container.
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’."