cgpRna

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

cgpRna provides pipelines, for RNA-Seq data, that implement commonly used mapping and analysis programs, such as TopHat and rna-star. At the present time (May 2016), only pipelines for mapping (with STAR), lane QC and fusion gene detection is included in this codebase.

Docker container

cgpRna is available as a Docker container on Quay.io.

Workflows on Dockstore

Due to an issue of Dockstore, we have not registered any of the workflows in cwl folder, as inputs of two of them are using two-dimensional arrays. Once the issue is resolved, we'll test our workflows with the newer release of Dockstore, register our workflows and list their registries here.

Dependencies and Installation

If you want to install cgpRna locally, you'll need to follow the instructions below, however, we recommend to use the Docker container.

Dependencies

cgpRna depends on these Perl packages, so they need to be installed first:

• PCAP-core
• VAGrENT
• cgpVcf
• Grass

Note: samtools is also a dependency but this is installed by PCAP-Core.

cgpRna uses RSeQC and its prerequisites are:

• gcc
• python3 and pip3 executable.
• R
• numpy

Installation

Once dependencies mentioned above are installed, run the following to install cgpRna:

./setup.sh path_to_install_to

N.B. the pathtoinstall_to should be the same as the install location used for PCAP-core and VAGrENT above.

Tools installed by setup.sh

• Some CPAN hosted libraries, see perl/Makefile.PL
• STAR
• Tophat
• deFuse
• RSeQC
• bowtie N.B. both bowtie and bowtie2 are installed and can be used with Tophat
• blat Unless already in the install location bin directory
• gmap The aligner used by deFuse
• faToTwoBit deFuse dependency
• bedtools Unless already in the install location bin directory
• blastn Used by tophat-fusion post
• HTSeq used for read counting

If you are planning to use the fusion pipeline, specifically defuse_fusion.pl, the deFuse config.txt file will need to be updated with the installed locations of a number of tools. These paths are printed to screen if the setup.sh script completes successfully so make a note of the locations and update the file as instructed.

LICENCE

``` Copyright (c) 2014-2019 Genome Research Ltd.

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

This file is part of cgpRna.

cgpRna 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’." ```