Merge branch 'hotfix/2.1.0'

CHANGES.md

@@ -0,0 +1,2 @@
+### 2.1.0
+* Added HTseq installer for read counting

README.md

@@ -69,7 +69,7 @@ N.B. the path_to_install_to should be the same as the install location used for
 * [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.

perl/lib/Sanger/CGP/CgpRna.pm

@@ -36,7 +36,7 @@ use strict;
 use Const::Fast qw(const);
 use base 'Exporter';
 
-our $VERSION = '2.0.18';
+our $VERSION = '2.1.0';
 our @EXPORT = qw($VERSION);
 
 1;

setup.sh

@@ -46,7 +46,8 @@ 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"
+VERSION_HTSEQ="0.6.0"
 
 done_message () {
     if [ $? -eq 0 ]; then
@@ -154,14 +155,14 @@ fi
 
 CHK2=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::Vagrent`
 if [[ "x$CHK2" == "x" ]] ; then
-  echo "PREREQUISITE: Please install VAGrENT before proceeding: https://github.com/cancerit/VAGrENT/releases"
-  exit 1;
+	echo "PREREQUISITE: Please install VAGrENT before proceeding: https://github.com/cancerit/VAGrENT/releases"
+	exit 1;
 fi
 
 CHK3=`perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' Sanger::CGP::Grass`
 if [[ "x$CHK3" == "x" ]] ; then
-  echo "PREREQUISITE: Please install Grass before proceeding: https://github.com/cancerit/grass/releases"
-  exit 1;
+	echo "PREREQUISITE: Please install Grass before proceeding: https://github.com/cancerit/grass/releases"
+	exit 1;
 fi
 
 #create a location to build dependencies
@@ -424,6 +425,23 @@ else
 fi
 done_message "" "Failed to build RSeQC."
 
+# install HTSeq
+echo -n "Installing HTSeq ..."
+if [ -e $SETUP_DIR/htseq.success ]; then
+  echo -n " previously installed ...";
+else
+(
+  cd $SETUP_DIR
+  get_distro "rseqc" $SOURCE_HTSEQ
+  mkdir -p htseq
+  tar --strip-components 1 -C htseq -zxf HTSeq-0.6.1p1.tar.gz 
+  cd $SETUP_DIR/htseq &&
+  python ./setup.py install --prefix=$INST_PATH
+  touch $SETUP_DIR/htseq.success
+  )>>$INIT_DIR/setup.log 2>&1
+fi
+done_message "" "Failed to build HTSeq."
+
 
 #add bin path for install tests
 export PATH="$INST_PATH/bin:$PATH"