From 93071a42628b4e009b8ed3ac12fd011732a7bb62 Mon Sep 17 00:00:00 2001
From: am26 <am26@sanger.ac.uk>
Date: Mon, 11 Apr 2016 20:18:40 +0100
Subject: [PATCH 1/4] Adding GTF default name in config.ini

---
 perl/config/star.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/perl/config/star.ini b/perl/config/star.ini
index 1bb209d..3772309 100755
--- a/perl/config/star.ini
+++ b/perl/config/star.ini
@@ -3,7 +3,7 @@ referencebuild=
 genebuild=
 species=
 referenceloc=
-gtffilename=
+gtffilename=ensembl.gtf
 normalfusionslist=normal-fusions
 starpath=
 starfusionpath=

From 8a93b773350447d7c2b0bbcaae15e12d92f87c35 Mon Sep 17 00:00:00 2001
From: am26 <am26@sanger.ac.uk>
Date: Mon, 11 Apr 2016 20:19:30 +0100
Subject: [PATCH 2/4] Adding latest version of Tophat

---
 setup.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/setup.sh b/setup.sh
index 5b36bbc..1efe181 100755
--- a/setup.sh
+++ b/setup.sh
@@ -37,7 +37,7 @@ SOURCE_BOWTIE1="https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/b
 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"
 VERSION_BOWTIE2="2.2.3"
-SOURCE_TOPHAT="http://ccb.jhu.edu/software/tophat/downloads/tophat-2.0.13.Linux_x86_64.tar.gz"
+SOURCE_TOPHAT="http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz"
 SOURCE_BLASTN="ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-x64-linux.tar.gz"
 SOURCE_DEFUSE="https://bitbucket.org/dranew/defuse/get/v0.7.0.tar.gz"
 VERSION_DEFUSE="0.7.0"
@@ -241,8 +241,8 @@ else
   mkdir -p tophat
   tar --strip-components 1 -C tophat -zxf tophat.tar.gz
   cd tophat
-  rm ./AUTHORS ./COPYING ./README 
-  cp ./* $INST_PATH/bin/.
+  rm ./AUTHORS ./README 
+  cp -r ./* $INST_PATH/bin/.
   touch $SETUP_DIR/tophat.success
   )>>$INIT_DIR/setup.log 2>&1
 fi

From 3da8721025eedd0d2d1e5ba895408a035a8961c6 Mon Sep 17 00:00:00 2001
From: am26 <am26@sanger.ac.uk>
Date: Mon, 11 Apr 2016 20:20:24 +0100
Subject: [PATCH 3/4] Adding junction.bed to tophat post run folders for latest
 version of Tophat

---
 perl/lib/Sanger/CGP/Tophat/Implement.pm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/perl/lib/Sanger/CGP/Tophat/Implement.pm b/perl/lib/Sanger/CGP/Tophat/Implement.pm
index 191d1bc..52c5bf3 100755
--- a/perl/lib/Sanger/CGP/Tophat/Implement.pm
+++ b/perl/lib/Sanger/CGP/Tophat/Implement.pm
@@ -417,6 +417,7 @@ sub split_setup {
 			make_path($split_dir) unless(-d $split_dir);
 			move($abs_tophat_rundir."/".$_ , $split_dir.'/fusions.out') or die "$!";
 			symlink($abs_tophat_rundir.'/accepted_hits.bam', $split_dir.'/accepted_hits.bam') unless(-l File::Spec->catfile($split_dir,'accepted_hits.bam'));
+			symlink($abs_tophat_rundir.'/junctions.bed', $split_dir.'/junctions.bed') unless(-l File::Spec->catfile($split_dir,'junctions.bed'));
 		}
 	}
 	

From 095dedb144ad02e95c8519c049f8888184166c66 Mon Sep 17 00:00:00 2001
From: am26 <am26@sanger.ac.uk>
Date: Mon, 11 Apr 2016 20:34:51 +0100
Subject: [PATCH 4/4] Upping version

---
 perl/lib/Sanger/CGP/CgpRna.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/perl/lib/Sanger/CGP/CgpRna.pm b/perl/lib/Sanger/CGP/CgpRna.pm
index 1c9e37f..feeecae 100644
--- a/perl/lib/Sanger/CGP/CgpRna.pm
+++ b/perl/lib/Sanger/CGP/CgpRna.pm
@@ -36,7 +36,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '2.0.7';
+our $VERSION = '2.0.8';
 our @EXPORT = qw($VERSION);
 
 1;