<commit_before># cgpRna

| Master                                        | Develop                                         |
| --------------------------------------------- | ----------------------------------------------- |
| [![Master Badge][travis-master]][travis-base] | [![Develop Badge][travis-develop]][travis-base] |

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 are included in this codebase.

## Docker contianer

cgpRna is available as a Docker container on [Quay.io][quay-repo].

[![Quay Badge][quay-status]][quay-repo]

## Workflows on Dockstore

Due to an [issue](https://github.com/dockstore/dockstore/issues/2923) of Dockstore, we have not registered any of the workflows in `cwl` folder, as inputs of two of them are using two-demensional arrays. Once the issue is resolved, we'll test our workflows with the newer release of Dockstore, regiester our workflows and list their registries here.

## Dependencies and Installation

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

### Dependencies

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

* [PCAP-core](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases)
* [VAGrENT](https://github.com/cancerit/VAGrENT/releases)
* [cgpVcf](https://github.com/cancerit/cgpVcf/releases)
* [Grass](https://github.com/cancerit/grass/releases)

cgpRna uses [RSeQC](http://rseqc.sourceforge.net/#installation) and its prerequisites are:

* gcc
* [python3](https://www.python.org/downloads/) and pip3 executable.
* [R](https://www.r-project.org/)
* [numpy](http://www.numpy.org/)

### Installation

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

```
./setup.sh path_to_install_to
```

N.B. the path_to_install_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](https://github.com/alexdobin/STAR/releases)
* [Tophat](https://ccb.jhu.edu/software/tophat/index.shtml)
* [deFuse](https://bitbucket.org/dranew/defuse)
* [RSeQC](http://rseqc.sourceforge.net)
* [bowtie](http://bowtie-bio.sourceforge.net/index.shtml) N.B. both bowtie and bowtie2 are installed and can be used with Tophat
* [blat](http://hgwdev.cse.ucsc.edu/~kent/src/) Unless already in the install location bin directory
* [gmap](http://research-pub.gene.com/gmap/) The aligner used by deFuse
* [faToTwoBit](http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/) deFuse dependency
* [bedtools](https://github.com/arq5x/bedtools2/) Unless already in the install location bin directory
* [blastn](http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) Used by tophat-fusion post
* [HTSeq](https://pypi.python.org/packages/3c/6e/f8dc3500933e036993645c3f854c4351c9028b180c6dcececde944022992/HTSeq-0.6.1p1.tar.gz) used for read counting
N.B. samtools is also a dependency but this is installed by PCAP-Core which should have already been installed (see above).

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 <<EMAIL>>
<commit_msg>minor rewording<commit_after># cgpRna

| Master                                        | Develop                                         |
| --------------------------------------------- | ----------------------------------------------- |
| [![Master Badge][travis-master]][travis-base] | [![Develop Badge][travis-develop]][travis-base] |

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 are included in this codebase.

## Docker contianer

cgpRna is available as a Docker container on [Quay.io][quay-repo].

[![Quay Badge][quay-status]][quay-repo]

## Workflows on Dockstore

Due to an [issue](https://github.com/dockstore/dockstore/issues/2923) of Dockstore, we have not registered any of the workflows in `cwl` folder, as inputs of two of them are using two-demensional arrays. Once the issue is resolved, we'll test our workflows with the newer release of Dockstore, regiester our workflows and list their registries here.

## Dependencies and Installation

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

### Dependencies

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

* [PCAP-core](https://github.com/ICGC-TCGA-PanCancer/PCAP-core/releases)
* [VAGrENT](https://github.com/cancerit/VAGrENT/releases)
* [cgpVcf](https://github.com/cancerit/cgpVcf/releases)
* [Grass](https://github.com/cancerit/grass/releases)

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

cgpRna uses [RSeQC](http://rseqc.sourceforge.net/#installation) and its prerequisites are:

* gcc
* [python3](https://www.python.org/downloads/) and pip3 executable.
* [R](https://www.r-project.org/)
* [numpy](http://www.numpy.org/)

### Installation

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

```
./setup.sh path_to_install_to
```

N.B. the path_to_install_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](https://github.com/alexdobin/STAR/releases)
* [Tophat](https://ccb.jhu.edu/software/tophat/index.shtml)
* [deFuse](https://bitbucket.org/dranew/defuse)
* [RSeQC](http://rseqc.sourceforge.net)
* [bowtie](http://bowtie-bio.sourceforge.net/index.shtml) N.B. both bowtie and bowtie2 are installed and can be used with Tophat
* [blat](http://hgwdev.cse.ucsc.edu/~kent/src/) Unless already in the install location bin directory
* [gmap](http://research-pub.gene.com/gmap/) The aligner used by deFuse
* [faToTwoBit](http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/) deFuse dependency
* [bedtools](https://github.com/arq5x/bedtools2/) Unless already in the install location bin directory
* [blastn](http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) Used by tophat-fusion post
* [HTSeq](https://pypi.python.org/packages/3c/6e/f8dc3500933e036993645c3f854c4351c9028b180c6dcececde944022992/HTSeq-0.6.1p1.tar.gz) 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 <<EMAIL>>

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