Can't build the wfmash dependency about pggb HOT 15 CLOSED

Ah, yes! I was indeed my conda that needed an update. I was finally able to create the environment and pggb is running now.
Thanks so much!

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It should be a gcc version problem (waveygang/wfmash#87 (comment)). Let us know!

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This is on x86_64-suse-linux. I tried it with gcc 9.3.0 and higher - same pthreads issue.

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@egoltsman Does the docker image work for you?

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@egoltsman Does the docker image work for you?

Unfortunately, I can't use docker in my environment due to a security policy.

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How about Bioconda or GUIX? https://odgi.readthedocs.io/en/latest/rst/installation.html offers a wide range of installation possibilities.

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@subwaystation : Sure, Conda would work. I'm building this as part of the pggb package, but the link you sent refers to odgi, which, as I understand is about graph visualizations. Can you comment?

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I somehow confused things. Sorry @egoltsman. We don't have a Bioconda package of wfmash, yet.

Maybe it is time to do so :)

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Hopefully, it will come soon bioconda/bioconda-recipes#29772

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@egoltsman It is on Bioconda https://anaconda.org/bioconda/wfmash. Does that solve your issue?

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Thank you for the conda package. Unfortunately, it's not liking my base environment which I just created from scratch. If I'm reading this correctly, different components of wfmash require different versions of the same library (e.g. libgcc-ng) ?

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package _libgcc_mutex conflicts for:
python=3.9 -> libgcc-ng[version='>=7.5.0'] -> _libgcc_mutex[version='*|0.1',build=main]
wfmash -> libgcc-ng[version='>=9.3.0'] -> _libgcc_mutex[version='*|0.1',build=main]

Package libstdcxx-ng conflicts for:
wfmash -> jemalloc[version='>=5.2.1'] -> libstdcxx-ng[version='>=7.3.0']
wfmash -> libstdcxx-ng[version='>=9.3.0']

Package libgcc-ng conflicts for:
wfmash -> libgcc-ng[version='>=9.3.0']
wfmash -> jemalloc[version='>=5.2.1'] -> libgcc-ng[version='>=7.2.0|>=7.3.0']The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.26=0
  - feature:|@/linux-64::__glibc==2.26=0
  - python=3.9 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
  - 

UPDATE: After I uninstalled all the offending packages conda still fails to reconcile the gcc version. Not sure what to do here as the versions it mentions are not actually in conflict:

UnsatisfiableError: The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.26=0
  - wfmash -> libgcc-ng[version='>=9.3.0'] -> __glibc[version='>=2.17']

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p.s. I could try to get a docker container running, but since I need wfmash as a dependency for pggb, I'm afraid I don't know how to link the two if the former is containerized.

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Hi @egoltsman

That's a weird error.
I just did conda create --name wfmash wfmash followed by conda activate wfmash and it works as expected.
Maybe you need to add wfmash to your environment first, then the other toolings? Or your base environment does not incorporate the most recent GCC toolchain of conda. They had some recent updates, that's maybe why you are still stuck with GCC v7.2 instead of GCC v9.3. Backwards compatibility might be tricky here.

We also have a docker image which contains all required pggb tools: https://github.com/pangenome/pggb#docker.

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