Ubuntu 18.04 install woes

[kdm9]

Hello Iqbal Lab folks!

I'm trying to get gramtools running on our Ubuntu 18.04 cluster, but having significant issues:

• install with the precompiled binaries fails, due to GLIBC/GLIBCXX version issues (18.04 glibc too old I assume)
• install from source fails, as the OS compiler toolchain is too old
• install from source within a conda env with updated dependencies and GCC/G++ fails, as cmake picks up the updated gcc but not the updated ar/ranlib, and conan doesn't even pick up the updated gcc. This leads to all sorts of fun errors during compilation.
• making a conda package fails, due to some strange linking error deep in conan-land. It seems like the cmake config hard-codes that conan is the source of the dependencies, which interferes with some conda dependencies and causes conflicting symbol names (e.g. regarding some zlib symbols in libhts.a).
• Using docker/singularity isn't supported on our infrastructure, so i can't do that.

Is there any approach I'm missing? Is there any chance gramtools can move to HBB, or similar static compilation toolchains as discussed in the original "static binaries" issue?

Best,
Kevin

[bricoletc]

Hi Kevin,

Thanks for raising this, and for logging everything you've tried. I will look into both compiling against older libc/something else than libc (musl) and making a bioconda package. Will update situation here!

[bricoletc]

Hi @kdm9 , could you try the latest release, v1.9.0?

I tried it in a Ubuntu 18.04 docker image and looks like it works 👍

Also, do you have a pointer to the conda recipe you used when trying to build a package for gramtools? It would be quite helpful- I've had a first go but have not gotten as far as you i think.

[kdm9]

Sorry, I forgot to say: this works perfectly on 18.04 now. Many thanks Brice!