Merge branch 'hotfix/5.4.2'

CHANGES.md

@@ -1,5 +1,10 @@
 # CHANGES
 
+## 5.4.2
+
+* use libdeflate /opt installation from cgpbigwig
+* performance now applies to samtools via this modification
+
 ## 5.4.1
 
 * Compile htslib with libdeflate (thanks to @mflevine)

Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/wtsicgp/cgpbigwig:1.5.0 as builder
+FROM quay.io/wtsicgp/cgpbigwig:1.5.1 as builder
 
 USER  root
 
@@ -11,7 +11,6 @@ ARG BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2
 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"
-ARG VER_LIBDEFLATE='v1.6'
 ARG VER_HTSLIB="1.11"
 ARG VER_SAMTOOLS="1.11"
 
@@ -63,7 +62,7 @@ FROM  ubuntu:20.04
 
 LABEL maintainer="[email protected]"\
       uk.ac.sanger.cgp="Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute" \
-      version="5.4.1" \
+      version="5.4.2" \
       description="pcap-core"
 
 ENV OPT /opt/wtsi-cgp

build/opt-build-local.sh

@@ -52,25 +52,18 @@ set -u
 cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH Const::Fast
 cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org -l $INST_PATH File::Which
 
-## libdeflate
-rm -rf tmp_deflate
-mkdir -p tmp_deflate
-curl -sSL --retry 10 https://github.com/ebiggers/libdeflate/archive/${VER_LIBDEFLATE}.tar.gz > distro.tar.gz
-tar --strip-components 1 -C tmp_deflate -zxf distro.tar.gz
-cd tmp_deflate
-make -j$CPU CFLAGS="-fPIC -O3" install
-PREFIX=$INST_PATH make -j$CPU CFLAGS="-fPIC -O3" install
-cd ../
-rm -rf distro.*
+export HTSLIB=$PWD/tmp_htslib # used after htslib block
 
-# won't build without "development" htslib structure:
+# won't build without "development" htslib structure due to need for static linking
 ## HTSLIB (tar.bz2)
-rm -rf tmp_htslib
-mkdir -p tmp_htslib
+rm -rf $HTSLIB
+mkdir -p $HTSLIB
 curl -sSL --retry 10 https://github.com/samtools/htslib/releases/download/${VER_HTSLIB}/htslib-${VER_HTSLIB}.tar.bz2 > distro.tar.bz2
-tar --strip-components 1 -C tmp_htslib -jxf distro.tar.bz2
-cd tmp_htslib
-./configure --enable-plugins --enable-libcurl --with-libdeflate --prefix=$INST_PATH
+tar --strip-components 1 -C $HTSLIB -jxf distro.tar.bz2
+cd $HTSLIB
+./configure --enable-plugins --enable-libcurl --with-libdeflate --prefix=$INST_PATH \
+  CPPFLAGS="-I$INST_PATH/include" \
+  LDFLAGS="-L${INST_PATH}/lib -Wl,-R${INST_PATH}/lib"
 make clean
 make -j$CPU
 cd ../
@@ -79,18 +72,16 @@ rm -rf distro.*
 make -C c clean
 export REF_CACHE=$PWD/t/data/ref_cache/%2s/%2s/%s
 export REF_PATH=$REF_CACHE
+make -C c -j$CPU prefix=$INST_PATH
 
-env HTSLIB=$PWD/tmp_htslib make -C c -j$CPU prefix=$INST_PATH
-env DEFLATE=$PWD/tmp_deflate
 cp bin/bam_stats $INST_PATH/bin/.
 cp bin/reheadSQ $INST_PATH/bin/.
 cp bin/diff_bams $INST_PATH/bin/.
 cp bin/mismatchQc $INST_PATH/bin/.
 cp bin/mmFlagModifier $INST_PATH/bin/.
 
 rm -rf $REF_CACHE
-rm -rf tmp_htslib
-rm -rf tmp_deflate
+rm -rf $HTSLIB
 
 cpanm --no-wget --no-interactive --notest --mirror http://cpan.metacpan.org --notest -l $INST_PATH --installdeps .
 cpanm -v --no-wget --no-interactive --mirror http://cpan.metacpan.org -l $INST_PATH .

c/Makefile

@@ -34,11 +34,10 @@ CFLAGS = -Wall
 HTSLOC?=$(HTSLIB)
 
 HTSTMP?=./htslib_tmp
-DEFLATETMP?=./deflate_tmp
 prefix=?/usr/local/
 
 #Define locations of header files
-OPTINC?= -I$(HTSLOC)/ -I/install_tmp/deflate_tmp/
+OPTINC?= -I$(HTSLOC)/
 INCLUDES= -I./ $(OPTINC) -rdynamic
 
 CAT_INCLUDES+= -I$(prefix)/include
@@ -47,7 +46,7 @@ CAT_LFLAGS+= -L$(prefix)/lib
 # define library paths in addition to /usr/lib
 #   if I wanted to include libraries not in /usr/lib I'd specify
 #   their path using -Lpath, something like:
-LFLAGS?= -L$(HTSTMP) -L$(DEFLATETMP)
+LFLAGS?= -L$(HTSTMP)
 
 # define any libraries to link into executable:
 #   if I want to link in libraries (libx.so or libx.a) I use the -llibname

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 = '5.4.1';
+our $VERSION = '5.4.2';
 our @EXPORT = qw($VERSION _which);
 
 const my $LICENSE =>

setup.sh

@@ -9,7 +9,6 @@ export BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0p
 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"
-export VER_LIBDEFLATE='v1.6'
 export VER_HTSLIB="1.11"
 export VER_SAMTOOLS="1.11"