Merge branch 'hotfix/5.5.1'

cancerit · Dec 10, 2020 · 69d082d · 69d082d
2 parents 4ed4ab8 + 44fc72c
commit 69d082d
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Showing 6 changed files with 11 additions and 4 deletions.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,10 @@
 # CHANGES
 
+## 5.5.1
+
+* `bwa-mem2` increment.
+* `bwa_mem2.pl` correct arg checking to catch failure to provide input files.
+
 ## 5.5.0
 
 * Update to bwa-mem2 production release (v2.1)

diff --git a/Dockerfile b/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_TAG="v2.1"
+ARG BWAMEM2_TAG="9cd69b3f383a5cbb5e47b9e08e4c11392e72a510"
 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"

diff --git a/bin/bwa_mem.pl b/bin/bwa_mem.pl
@@ -199,6 +199,7 @@ sub setup {
   $opts{'tmp'} = $tmpdir;
 
   my $cwd = cwd();
+  $opts{'raw_files'} = [];
   for(@ARGV) {
     $_ = "$cwd/$_" unless($_ =~ m|^/|);
     push @{$opts{'raw_files'}}, $_;

diff --git a/build/opt-build.sh b/build/opt-build.sh
@@ -117,8 +117,9 @@ fi
 ## build BWA-mem2 (tar.gz)
 if [ ! -e $SETUP_DIR/bwa2.success ]; then
   rm -rf distro
-  git clone --branch v2.1 --recursive --depth 1 https://github.com/bwa-mem2/bwa-mem2.git distro
+  git clone --recursive https://github.com/bwa-mem2/bwa-mem2.git distro
   cd distro
+  git checkout $BWAMEM2_TAG
   make -j$CPU multi
   cp bwa-mem2* $INST_PATH/bin/.
   cd ../

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 = '5.5.0';
+our $VERSION = '5.5.1';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>

diff --git a/setup.sh b/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_TAG="v2.1"
+export BWAMEM2_TAG="9cd69b3f383a5cbb5e47b9e08e4c11392e72a510"
 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"