Merge branch 'release/5.6.0'

cancerit · Mar 17, 2021 · 4fe6bd5 · 4fe6bd5
2 parents 69d082d + 36b2aab
commit 4fe6bd5
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Showing 5 changed files with 13 additions and 5 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,10 @@
 # CHANGES
 
+## 5.6.0
+
+* `bwa-mem2` updated to v2.2.1 following successful large scale testing
+  * [please see here](https://github.com/bwa-mem2/bwa-mem2/issues/109).
+
 ## 5.5.1
 
 * `bwa-mem2` increment.

diff --git a/Dockerfile b/Dockerfile
@@ -7,7 +7,9 @@ USER  root
 
 # newer gitlab versions do not work
 ARG BBB2_URL="https://gitlab.com/german.tischler/biobambam2/uploads/178774a8ece96d2201fcd0b5249884c7/biobambam2-2.0.146-release-20191030105216-x86_64-linux-gnu.tar.xz"
-ARG BWAMEM2_TAG="9cd69b3f383a5cbb5e47b9e08e4c11392e72a510"
+ARG BWAMEM2_GIT="https://github.com/bwa-mem2/bwa-mem2.git"
+# accepts tags or commmit ids
+ARG BWAMEM2_TAG="v2.2.1"
 ARG STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz"
 ARG VER_BIODBHTS="3.01"
 ARG VER_BWA="v0.7.17"
@@ -64,7 +66,6 @@ FROM  ubuntu:20.04
 
 LABEL maintainer="[email protected]"\
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \
-      version="5.5.0" \
       description="pcap-core"
 
 ENV OPT /opt/wtsi-cgp

diff --git a/build/opt-build.sh b/build/opt-build.sh
@@ -117,7 +117,7 @@ fi
 ## build BWA-mem2 (tar.gz)
 if [ ! -e $SETUP_DIR/bwa2.success ]; then
   rm -rf distro
-  git clone --recursive https://github.com/bwa-mem2/bwa-mem2.git distro
+  git clone --recursive $BWAMEM2_GIT distro
   cd distro
   git checkout $BWAMEM2_TAG
   make -j$CPU multi

diff --git a/lib/PCAP.pm b/lib/PCAP.pm
@@ -28,7 +28,7 @@ use FindBin qw($Bin);
 use File::Which qw(which);
 # don't use autodie, only core perl in here
 
-our $VERSION = '5.5.1';
+our $VERSION = '5.6.0';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>

diff --git a/setup.sh b/setup.sh
@@ -5,7 +5,9 @@
 
 # newer gitlab versions do not work
 export BBB2_URL="https://gitlab.com/german.tischler/biobambam2/uploads/178774a8ece96d2201fcd0b5249884c7/biobambam2-2.0.146-release-20191030105216-x86_64-linux-gnu.tar.xz"
-export BWAMEM2_TAG="9cd69b3f383a5cbb5e47b9e08e4c11392e72a510"
+export BWAMEM2_GIT="https://github.com/bwa-mem2/bwa-mem2.git"
+# accepts tags or commmit ids
+export BWAMEM2_TAG="v2.2.1"
 export STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz"
 export VER_BIODBHTS="3.01"
 export VER_BWA="v0.7.17"