Merge branch 'release/5.5.0'

CHANGES.md

@@ -1,5 +1,9 @@
 # CHANGES
 
+## 5.5.0
+
+* Update to bwa-mem2 production release (v2.1)
+
 ## 5.4.2
 
 * use libdeflate /opt installation from cgpbigwig

Dockerfile

@@ -7,7 +7,7 @@ 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_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2"
+ARG BWAMEM2_TAG="v2.1"
 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"
@@ -37,6 +37,8 @@ RUN apt-get install -yq --no-install-recommends libdb-dev
 RUN apt-get install -yq --no-install-recommends libgnutls28-dev
 RUN apt-get install -yq --no-install-recommends xz-utils
 RUN apt-get install -yq --no-install-recommends libexpat1-dev
+RUN apt-get install -yq --no-install-recommends git
+RUN apt-get install -yq --no-install-recommends g++
 
 RUN locale-gen en_US.UTF-8
 RUN update-locale LANG=en_US.UTF-8
@@ -62,7 +64,7 @@ FROM  ubuntu:20.04
 
 LABEL maintainer="[email protected]"\
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \
-      version="5.4.2" \
+      version="5.5.0" \
       description="pcap-core"
 
 ENV OPT /opt/wtsi-cgp

build/opt-build.sh

@@ -116,10 +116,12 @@ fi
 
 ## build BWA-mem2 (tar.gz)
 if [ ! -e $SETUP_DIR/bwa2.success ]; then
-  curl -sSL $BWAMEM2_URL > distro.tar.bz2
-  rm -rf distro/*
-  tar --strip-components 1 -C distro -jxf distro.tar.bz2
-  cp distro/bwa-mem2* $INST_PATH/bin/.
+  rm -rf distro
+  git clone --branch v2.1 --recursive --depth 1 https://github.com/bwa-mem2/bwa-mem2.git distro
+  cd distro
+  make -j$CPU multi
+  cp bwa-mem2* $INST_PATH/bin/.
+  cd ../
   rm -rf distro.* distro/*
   touch $SETUP_DIR/bwa2.success
 fi

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 = '5.4.2';
+our $VERSION = '5.5.0';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>

setup.sh

@@ -5,7 +5,7 @@
 
 # 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_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2"
+export BWAMEM2_TAG="v2.1"
 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"