From 55d5cf92526823a61b9e1687e293f4c118a9be7a Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Tue, 6 Oct 2020 18:15:08 +0000
Subject: [PATCH 1/2] htslib with installed libdeflate, issues with cgpbigwig
 compile to resolve

---
 Dockerfile         |  1 +
 build/opt-build.sh | 18 +++++++++++++++++-
 setup.sh           |  1 +
 3 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index d560cc9..ecef110 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -6,6 +6,7 @@ USER  root
 # need to keep in sync with setup.sh
 ARG VER_HTSLIB="1.11"
 ARG VER_LIBBW="0.4.4"
+ARG VER_LIBDEFLATE="v1.6"
 
 ENV OPT /opt/wtsi-cgp
 ENV PATH $OPT/bin:$PATH
diff --git a/build/opt-build.sh b/build/opt-build.sh
index a4b0325..ada5730 100755
--- a/build/opt-build.sh
+++ b/build/opt-build.sh
@@ -52,6 +52,19 @@ set -u
 
 ##### DEPS for cgpBigWig #####
 
+## libdeflate
+if [ ! -e $SETUP_DIR/libdeflate.success ]; then
+  rm -rf tmp_deflate
+  mkdir -p tmp_deflate
+  curl -sSL --retry 10 https://github.com/ebiggers/libdeflate/archive/${VER_LIBDEFLATE}.tar.gz > distro.tar.gz
+  tar --strip-components 1 -C tmp_deflate -zxf distro.tar.gz
+  cd tmp_deflate
+  PREFIX=$INST_PATH make -j$CPU CFLAGS="-fPIC -O3" install
+  cd ../
+  rm -rf distro.* tmp_deflate
+  touch $SETUP_DIR/libdeflate.success
+fi
+
 ## HTSLIB (tar.bz2)
 if [ ! -e $SETUP_DIR/htslib.success ]; then
   rm -rf htslib
@@ -59,7 +72,10 @@ if [ ! -e $SETUP_DIR/htslib.success ]; then
   curl -sSL --retry 10 https://github.com/samtools/htslib/releases/download/${VER_HTSLIB}/htslib-${VER_HTSLIB}.tar.bz2 > distro.tar.bz2
   tar --strip-components 1 -C htslib -jxf distro.tar.bz2
   cd htslib
-  ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH
+  ./configure --enable-plugins --enable-libcurl --prefix=$INST_PATH \
+    --with-libdeflate \
+    CPPFLAGS="-I$INST_PATH/include" \
+    LDFLAGS="-L${INST_PATH}/lib -Wl,-R${INST_PATH}/lib"
   make clean
   make -j$CPU
   make install
diff --git a/setup.sh b/setup.sh
index 7024d29..cbe646d 100755
--- a/setup.sh
+++ b/setup.sh
@@ -36,6 +36,7 @@
 # need to keep in sync with Dockerfile
 export VER_HTSLIB="1.11"
 export VER_LIBBW="0.4.4"
+export VER_LIBDEFLATE="v1.6"
 
 if [[ ($# -ne 1 && $# -ne 2) ]] ; then
   echo "Please provide an installation path and optionally perl lib paths to allow, e.g."

From 6205fdeb6a3b855501179151c8a94c3e4cff6bdc Mon Sep 17 00:00:00 2001
From: Keiran Raine <kr2@sanger.ac.uk>
Date: Wed, 7 Oct 2020 08:57:20 +0000
Subject: [PATCH 2/2] Now builds correctly with some extra flags

---
 build/opt-build-local.sh | 1 +
 c/Makefile               | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/build/opt-build-local.sh b/build/opt-build-local.sh
index 028cae3..209b2a9 100755
--- a/build/opt-build-local.sh
+++ b/build/opt-build-local.sh
@@ -46,6 +46,7 @@ export MANPATH=`echo $INST_PATH/man:$INST_PATH/share/man:$MANPATH | perl -pe 's/
 set -u
 
 ##### cgpBigWig installation
+export LFLAGS="-L${INST_PATH}/lib"
 make -C c clean
 make -C c -j$CPU prefix=$INST_PATH HTSLIB=$INST_PATH/lib
 cp bin/bam2bedgraph $INST_PATH/bin/.
diff --git a/c/Makefile b/c/Makefile
index a877fc1..a9f628b 100644
--- a/c/Makefile
+++ b/c/Makefile
@@ -42,8 +42,8 @@ LFLAGS?= -L$(HTSTMP)
 # define any libraries to link into executable:
 #   if I want to link in libraries (libx.so or libx.a) I use the -llibname
 #   option, something like (this will link in libmylib.so and libm.so:
-LIBS =-lhts -lpthread -lz -lbz2 -llzma -lm -ldl
-LIBBWLIBS=-lBigWig -lz -lbz2 -llzma -lcurl -lm -lgnutls -ltasn1 -lhogweed -lnettle -lgmp -lp11-kit
+LIBS =-lhts -lpthread -lz -lbz2 -llzma -lm -ldl -ldeflate
+LIBBWLIBS=-lBigWig -lz -lbz2 -llzma -lcurl -lm -lgnutls -ltasn1 -lhogweed -lnettle -lgmp -lp11-kit -ldeflate
 
 # define the C source files
 #SRCS = ./bam_access.c ./bam_stats_output.c ./bam_stats_calcs.c