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for setting up htslib

downloade glibz source

./configure --prefix=${CONDA_PREFIX} make install

Actually trying conda only, that is avoiding compiling gzip. Previous issue was in ./configure step

conda install zlib conda install -c anaconda bzip2 #conda install -c anaconda xz

conda install -c rdonnelly xz-devel-amzn2-aarch64

conda install zlib bzip2 xz libcurl

get htslib as a submodule

git submodule update --init --recursive

with gdb debug flags

CPPFLAGS="-ggdb -Wall -O2 -fvisibility=hidden -I${CONDA_PREFIX}/include" LDFLAGS="-L${CONDA_PREFIX}/lib" ./configure --prefix=${CONDA_PREFIX} CPPFLAGS="-ggdb -Wall -O2 -fvisibility=hidden -I${CONDA_PREFIX}/include" LDFLAGS="-L${CONDA_PREFIX}/lib" ./configure --prefix=${CONDA_PREFIX} --disable-lzma --enable-gcs

most recently run. I'm not sure if rpath and Pkg-config are doing anything. At higher level I was adding rpath-link, still works as of 07-27-24

#CFLAGS="-ggdb -Wall -O2 -I${CONDA_PREFIX}/include -L${CONDA_PREFIX}/lib" LDFLAGS="-Wl,-rpath,${CONDA_PREFIX}/lib" PKG_CONFIG_PATH="${CONDA_PREFIX}/lib/pkgconfig/" ./configure --prefix=${CONDA_PREFIX} --disable-lzma --enable-gcs CFLAGS="-ggdb -Wall -O2 -I${CONDA_PREFIX}/include -L${CONDA_PREFIX}/lib" LDFLAGS="-Wl,-rpath,${CONDA_PREFIX}/lib" PKG_CONFIG_PATH="${CONDA_PREFIX}/lib/pkgconfig/" ./configure --prefix=${CONDA_PREFIX} --enable-gcs

make && make install

one test where I could compile against my installed htslib

https://stackoverflow.com/questions/6562403/i-dont-understand-wl-rpath-wl

this doesn't work, with same linker error I've been seeing elsewhere.

g++ -I ../../envs/include/ -L../../envs/lib test.cpp -lhts

including rpath works

g++ -I ../../envs/include/ -L../../envs/lib test.cpp -Wl,-rpath,../../envs/lib -lhts

rpath with CONDA_PREFIX doesn't work

g++ -I ../../envs/include/ -L${CONDA_PREFIX}/lib -Wl,-rpath,${CONDA_PREFIX}/lib test.cpp -lhts

rpath-link with CONDA_PREFIX does work

g++ -I ../../envs/include/ -L${CONDA_PREFIX}/lib -Wl,-rpath-link,${CONDA_PREFIX}/lib test.cpp -lhts

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