Sentieon docker image #3348
Sentieon docker image #3348
Conversation
| - profile: "conda" | ||
| - profile: "singularity" | ||
| tags: sentieon/bwamem | ||
| - profile: "conda" | ||
| - profile: "singularity" |
There was a problem hiding this comment.
Sentieon on conda works fine, Sentieon on singularity has a problem with LD_LIBRARY_PATH. It should be fine on most machines but doesn't work on the GHA runners. See here for when I fixed the problem: bioconda/bioconda-recipes#38781
There was a problem hiding this comment.
I can't run Sentieon with the singularity images introduced in this PR. I get the now well-known:
error while loading shared libraries: libstdc++.so.6: cannot open shared object file: No such file or directory
Similar issue with the subsequent images made by Don for Sentieon 202112.07.
I'm afraid this is a showstopper for this PR 😬
There was a problem hiding this comment.
Darn!!! I don't know how singularity containers are built, where do they inherit LD_LIBRARY from?
Has been for a while: https://github.com/bioconda/bioconda-recipes/tree/master/recipes/sentieon |
|
Not needed anymore |
Replace Sentieon Docker image with one from Quay.io
There might be a good reason for not using quay.io, but it's worth a try.