Merge branch 'release/2.2.0'

.gitignore

@@ -4,9 +4,8 @@
 /perl/pm_to_blib
 /install_tmp
 /setup.log
-/LICENSE
-/README.md
 /perl/MYMETA.json
 /perl/MYMETA.yml
 /perl/docs/
 /perl/perltidy.LOG
+/env

CHANGES.md

@@ -1,23 +1,39 @@
-### 2.1.9
+# CHANGES
+
+## 2.2.0
+
+* RSeqQC  - Updated to 2.6.4, fixes known issues with low levels of mapped data.
+  * Also resolves 2.6.3 that is no longer available from central repos.
+* HTSeq - updated to 0.7.2 to ensure compatilbility with current pysam.
+
+## 2.1.9
+
 * Fix missed compilation failure
 
-### 2.1.8
+## 2.1.8
+
 * Fix issues with empty output from tophatpost when running tophat_filter
 
-### 2.1.6-2.1.7
+## 2.1.6-2.1.7
+
 * Fixing issues with data exhibiting no fusions.
 
-### 2.1.5
+## 2.1.5
+
 * updating cpanm source url
 
-### 2.1.4
+## 2.1.4
+
 * Fixing installation of tophat. Since we no longer use a compiled repository. Bug introduced in 2.1.2.
 
-### 2.1.3
+## 2.1.3
+
 * Correct name from sample.bas to sample.bam.bas
 
-### 2.1.2
+## 2.1.2
+
 * Fixed tophat-fusion-post issue in local tophat fork added tophat v2.1.0a to setup.sh
 
-### 2.1.1
+## 2.1.1
+
 * Added HTseq installer for read counting

README.md

@@ -1,58 +1,35 @@
-LICENCE
-=======
+# cgpRna
 
-Copyright (c) 2014-2015 Genome Research Ltd.
-
-Author: Cancer Genome Project <[email protected]>
-
-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’."
-
-cgpRna
-======
-
-cgpRna provides pipelines, for RNA-Seq data, that implement commonly used mapping 
+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 
+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.
 
-### Dependencies/Installation
+## Dependencies and Installation
+
+Please install Perl packages:
 
-Please install Perl packages [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) and [Grass](https://github.com/cancerit/grass/releases) 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.
 
 Prerequisites for the [RSeQC](http://rseqc.sourceforge.net/#installation) software are:
+
 * gcc
-* [python2.7](https://www.python.org/downloads/) (The minimum version the pipeline has been tested with is python-2.7.6
+* [python2.7](https://www.python.org/downloads/)
+  * The minimum version the pipeline has been tested with is python-2.7.6
 * [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:
 
+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:
+
+```
 ./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.
 
@@ -72,5 +49,40 @@ N.B. the path_to_install_to should be the same as the install location used for
 * [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.
+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) 2014-2017 Genome Research Ltd.
+
+Author: Cancer Genome Project <[email protected]>
+
+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’."
+```

perl/lib/Sanger/CGP/CgpRna.pm

@@ -36,7 +36,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '2.1.9';
+our $VERSION = '2.2.0';
 our @EXPORT = qw($VERSION);
 
 1;

setup.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 ########## LICENCE ##########
-# Copyright (c) 2014-2016 Genome Research Ltd.
+# Copyright (c) 2014-2017 Genome Research Ltd.
 #
 # Author: Cancer Genome Project <[email protected]>
 #
@@ -33,7 +33,6 @@
 
 SOURCE_STAR="https://github.com/alexdobin/STAR/archive/2.5.0c.tar.gz"
 SOURCE_STARFUSION="https://github.com/STAR-Fusion/STAR-Fusion/archive/v0.1.1.tar.gz"
-SOURCE_RSEQC="http://sourceforge.net/projects/rseqc/files/RSeQC-2.6.3.tar.gz/download"
 SOURCE_BOWTIE1="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/bowtie-1.1.1-linux-x86_64.zip/download"
 VERSION_BOWTIE1="1.1.1"
 SOURCE_BOWTIE2="https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.3/bowtie2-2.2.3-linux-x86_64.zip/download"
@@ -46,7 +45,8 @@ SOURCE_GMAP="http://research-pub.gene.com/gmap/src/gmap-gsnap-2015-09-10.tar.gz"
 SOURCE_BLAT="http://users.soe.ucsc.edu/~kent/src/blatSrc35.zip"
 SOURCE_FATOTWOBIT="http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit"
 SOURCE_BEDTOOLS="https://github.com/arq5x/bedtools2/releases/download/v2.21.0/bedtools-2.21.0.tar.gz"
-SOURCE_HTSEQ="https://pypi.python.org/packages/3c/6e/f8dc3500933e036993645c3f854c4351c9028b180c6dcececde944022992/HTSeq-0.6.1p1.tar.gz"
+RSEQC_VERSION=2.6.4
+HTSEQ_VERSION=0.7.2
 
 done_message () {
     if [ $? -eq 0 ]; then
@@ -417,11 +417,7 @@ if [ -e $SETUP_DIR/rseqc.success ]; then
 else
 (
   cd $SETUP_DIR
-  get_distro "rseqc" $SOURCE_RSEQC
-  mkdir -p rseqc
-  tar --strip-components 1 -C rseqc -zxf rseqc.tar.gz
-  cd $SETUP_DIR/rseqc &&
-  python ./setup.py install --prefix=$INST_PATH
+  pip install --prefix $INST_PATH RSeQC==$RSEQC_VERSION
   touch $SETUP_DIR/rseqc.success
   )>>$INIT_DIR/setup.log 2>&1
 fi
@@ -434,11 +430,7 @@ if [ -e $SETUP_DIR/htseq.success ]; then
 else
 (
   cd $SETUP_DIR
-  get_distro "htseq" $SOURCE_HTSEQ
-  mkdir -p htseq
-  tar --strip-components 1 -C htseq -zxf htseq.tar.gz
-  cd $SETUP_DIR/htseq &&
-  python ./setup.py install --prefix=$INST_PATH
+  pip install --prefix $INST_PATH HTSeq==$HTSEQ_VERSION
   touch $SETUP_DIR/htseq.success
   )>>$INIT_DIR/setup.log 2>&1
 fi