Opening this error to document our recent attempts to build the image using the Dockerfile on quay's servers.
It seems the main problem is building revbayes from scratch - more specifically the massive amount of compute time needed when building the boost libraries. I pushed to a branch which solved the quay build by downloading a pre-compiled executable. However, this (unsurprisingly in hindsight) introduced a cross-compilation error when running:
root@4a5fbddf309a:/linearham# ./test.sh
scons: Reading SConscript files ...
Mkdir("output")
scons: done reading SConscript files.
scons: Building targets ...
git rev-parse --verify HEAD >> output/git.log && git describe --dirty --always >> output/git.log
lib/partis/bin/partis annotate --all-seqs-simultaneous --infname data/liao_dataset.fasta --parameter-dir output/parameter_dir --locus igh --extra-annotation-columns linearham-info --outfname output/partis_run.yaml > output/partis_run.stdout.log
scons: done building targets.
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
scripts/parse_cluster.py output/partis_run.yaml --indel-reversed-seqs --seed-seq KC576081.1 --fasta-output-file output/cluster-0/lineage_KC576081.1/cluster_seqs.fasta --yaml-output-file output/cluster-0/lineage_KC576081.1/cluster.yaml
only one annotation in partis output file. Using it.
writing 313 sequences to output/cluster-0/lineage_KC576081.1/cluster_seqs.fasta
scripts/generate_revbayes_rev_file.py templates/revbayes_template.rev --fasta-path output/cluster-0/lineage_KC576081.1/cluster_seqs.fasta --mcmc-iter 25 --mcmc-thin 1 --tune-iter 0 --tune-thin 100 --num-rates 4 --seed 0 --output-path output/cluster-0/lineage_KC576081.1/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/revbayes_run.rev
lib/revbayes/projects/cmake/rb output/cluster-0/lineage_KC576081.1/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/revbayes_run.rev > output/cluster-0/lineage_KC576081.1/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/revbayes_run.stdout.log
lib/revbayes/projects/cmake/rb: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by lib/revbayes/projects/cmake/rb)
lib/revbayes/projects/cmake/rb: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by lib/revbayes/projects/cmake/rb)
scons: *** [output/cluster-0/lineage_KC576081.1/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/revbayes_run.trees] Error 1
scons: building terminated because of errors.
Ultimately, we decided the best option was to let the gh action build and push the image to the quay repo was a fine solution, so we'll disable the triggers in quay, and must be careful to choose the correct tag when pulling images from the repository. The ones prefixed by "V" are the ones you want pertaining to a commit.
Opening this error to document our recent attempts to build the image using the Dockerfile on quay's servers.
It seems the main problem is building revbayes from scratch - more specifically the massive amount of compute time needed when building the boost libraries. I pushed to a branch which solved the quay build by downloading a pre-compiled executable. However, this (unsurprisingly in hindsight) introduced a cross-compilation error when running:
Ultimately, we decided the best option was to let the gh action build and push the image to the quay repo was a fine solution, so we'll disable the triggers in quay, and must be careful to choose the correct tag when pulling images from the repository. The ones prefixed by "V" are the ones you want pertaining to a commit.