Cannot build genomicsbench

[rwk-unil]

Hello,
I am trying to build and run genomicsbench but the build fails.
I am running on Ubuntu 22.04.4 LTS x86_64 with Linux kernel 6.5.13.

I did the following :

git clone --recursive https://github.com/arun-sub/genomicsbench.git
cd genomicsbench/
sudo apt install $(cat debian.prerequisites)
make -j$(nproc)

• First, I encountered an issue with bwa-mem2 because it defines __rdtsc which is now defined by the compiled, see : Redefinition of __rdtsc breaks modern GCC bwa-mem2/bwa-mem2#207 removing the definition allowed to build bwa-mem2.
• Second, I had to add -ldeflate in the linker flags in the benchmarks/dbg/Makefile.
• I also had to set JAVA_AWT_INCLUDE_PATH in tools/GKL/CMakeLists.txt.

Now, the build goes up to :

...
cd tools/GKL; ./gradlew test

> Task :cmakeBuild
configure.ac:37: warning: The macro `AC_PROG_CC_STDC' is obsolete.
configure.ac:37: You should run autoupdate.
./lib/autoconf/c.m4:1666: AC_PROG_CC_STDC is expanded from...
configure.ac:37: the top level
configure.ac:23: installing 'build-aux/compile'
configure.ac:12: installing 'build-aux/missing'
Makefile.am: installing 'build-aux/depcomp'
make[3]: *** [src/main/native/compression/CMakeFiles/isalExternal.dir/build.make:120: src/main/native/compression/isalExternal-prefix/src/isalExternal-stamp/isalExternal-patch] Error 1
make[2]: *** [CMakeFiles/Makefile2:192: src/main/native/compression/CMakeFiles/isalExternal.dir/all] Error 2
make[1]: *** [Makefile:136: all] Error 2

> Task :cmakeBuild FAILED

FAILURE: Build failed with an exception.

* What went wrong:
Execution failed for task ':cmakeBuild'.
> Process 'command 'make'' finished with non-zero exit value 2

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 2s
3 actionable tasks: 1 executed, 2 up-to-date
make: *** [Makefile:18: all] Error 1

and fails. I don't know how to solve this.

Any insights would be appreciated. Also if there is a Docker file or image for these benchmarks it would be great and make things easier to setup and replicate.

Thank you for your help,
Best regards,
Rick