Merge branch 'release/2.5.0'

* Added run-cgprna subcommands: `tophat-fusion`, `start-fusion` and `defuse` to run infuse pipeline.
* Re-organized expected file structure in Star reference bundle. Previous Star reference bundle on the FTP server will not work for this version.
* Added CWL files to run Infuse pipeline in cgpRna and example JSON files for using them with Dockstore.
* Uploaded new set of reference bundle files for GRCh38 and GRCh37d5 to the FTP server.
* Updated `setup.sh` to install Python3 RSeQC and HTSeq.

Author: Yaobo Xu

CHANGES.md

@@ -1,5 +1,13 @@
 # CHANGES
 
+## 2.5.0
+
+* Added run-cgprna subcommands: `tophat-fusion`, `start-fusion` and `defuse` to run infuse pipeline.
+* Re-organized expected file structure in Star reference bundle. Previous Star reference bundle on the FTP server will not work for this version.
+* Added CWL files to run Infuse pipeline in cgpRna and example JSON files for using them with Dockstore.
+* Uploaded new set of reference bundle files for GRCh38 and GRCh37d5 to the FTP server.
+* Updated `setup.sh` to install Python3 RSeQC and HTSeq.
+
 ## 2.4.1
 
 * added a patched topaht-fusion-post script, in which the contig name bug #37 is fixed

Dockerfile

@@ -91,7 +91,7 @@ FROM ubuntu:16.04
 
 LABEL maintainer="[email protected]" \
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute" \
-      version="2.4.1" \
+      version="2.5.0" \
       description="cgpRna docker"
 
 # Version of tools that are installed in both stages, make sure they are consistent.
@@ -139,7 +139,7 @@ RUN locale-gen en_US.UTF-8
 RUN update-locale LANG=en_US.UTF-8
 
 ENV OPT /opt/wtsi-cgp
-ENV PATH $OPT/bin:$OPT/biobambam2/bin:$OPT/python-lib/bin/:$PATH
+ENV PATH $OPT/bin:$OPT/biobambam2/bin:$OPT/python-lib/bin:$PATH
 ENV PERL5LIB $OPT/lib/perl5
 ENV R_LIBS $OPT/R-lib
 ENV R_LIBS_USER $R_LIBS

README.md

@@ -1,37 +1,49 @@
 # cgpRna
 
-[![Quay Badge][quay-status]][quay-repo]
-
 | 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 but this will be added
-to over time with; differential expression, gene/transcript quantification, splice
-variant analysis and allele specific expression.
+and fusion gene detection is included in this codebase.
+
+## Docker container
+
+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-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
 
-Please install Perl packages:
+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](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) first.
+* [Grass](https://github.com/cancerit/grass/releases)
+
+Note: samtools is also a dependency but this is installed by PCAP-Core.
 
-Prerequisites for the [RSeQC](http://rseqc.sourceforge.net/#installation) software are:
+cgpRna uses [RSeQC](http://rseqc.sourceforge.net/#installation) and its prerequisites are:
 
 * gcc
-* [python2.7](https://www.python.org/downloads/)
-  * The minimum version the pipeline has been tested with is python-2.7.6
+* [python3](https://www.python.org/downloads/) and pip3 executable.
 * [R](https://www.r-project.org/)
 * [numpy](http://www.numpy.org/)
 
-Once that is done and your $PATH environment variable has been updated so that newly installed
-software can be found, run the following to install cgpRna:
+### Installation
+
+Once dependencies mentioned above are installed, run the following to install cgpRna:
 
 ```
 ./setup.sh path_to_install_to
@@ -53,7 +65,6 @@ N.B. the path_to_install_to should be the same as the install location used for
 * [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.
@@ -63,7 +74,7 @@ the locations and update the file as instructed.
 ## LICENCE
 
 ```
-Copyright (c) 2014-2017 Genome Research Ltd.
+Copyright (c) 2014-2019 Genome Research Ltd.
 
 Author: Cancer Genome Project <[email protected]>