Merge branch 'release/2.0.8'

cancerit · Apr 11, 2016 · 1836e65 · 1836e65
2 parents aa34ff4 + 095dedb
commit 1836e65
Show file tree

Hide file tree

Showing 4 changed files with 6 additions and 5 deletions.
diff --git 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=

diff --git 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;
diff --git 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'));
 		}
 	}
 

diff --git 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