Update Nextclade: Enable linux-aarch64

[corneliusroemer]

https://app.circleci.com/pipelines/github/bioconda/bioconda-recipes/109939/workflows/d6e1d687-5cdc-4c5d-865a-1ba0cb41b932/jobs/180788?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-checks-link&utm_content=summary

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[corneliusroemer]

Not sure why this happens, it's the same build script as for linux64 which passes:

15:17:25 BIOCONDA INFO (OUT) The following NEW packages will be INSTALLED:
15:17:25 BIOCONDA INFO (OUT) 
15:17:25 BIOCONDA INFO (OUT)     nextclade: 3.3.0-h23ed54d_1 local
15:17:25 BIOCONDA INFO (OUT) 
15:17:25 BIOCONDA INFO (OUT) Preparing transaction: ...working... done
15:17:27 BIOCONDA INFO (OUT) Verifying transaction: ...working... done
15:17:27 BIOCONDA INFO (OUT) Executing transaction: ...working... done
15:17:27 BIOCONDA INFO (OUT) export PREFIX=/opt/conda/conda-bld/nextclade_1709651729143/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol
15:17:27 BIOCONDA INFO (OUT) export SRC_DIR=/opt/conda/conda-bld/nextclade_1709651729143/test_tmp
15:17:28 BIOCONDA INFO (OUT) + set -e
15:17:28 BIOCONDA INFO (OUT) ++ echo 3.3.0
15:17:28 BIOCONDA INFO (OUT) ++ cut -d. -f1
15:17:28 BIOCONDA INFO (OUT) + MAJOR_VERSION=3
15:17:28 BIOCONDA INFO (OUT) + for BIN in nextclade 'nextclade$MAJOR_VERSION'
15:17:28 BIOCONDA INFO (OUT) + nextclade --version
15:17:28 BIOCONDA INFO (OUT) nextclade: relocation error: nextclade: symbol __cxa_thread_atexit_impl, version GLIBC_2.18 not defined in file libc.so.6 with link time reference
15:17:29 BIOCONDA INFO (OUT) Tests failed for nextclade-3.3.0-h23ed54d_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken
15:17:29 BIOCONDA INFO (OUT) WARNING:conda_build.build:Tests failed for nextclade-3.3.0-h23ed54d_1.tar.bz2 - moving package to /opt/conda/conda-bld/broken
15:17:29 BIOCONDA INFO (OUT) TESTS FAILED: nextclade-3.3.0-h23ed54d_1.tar.bz2
15:17:33 BIOCONDA ERROR COMMAND FAILED (exited with 1): docker run -t --net host --rm -v /tmp/tmpifmzybis/build_script.bash:/opt/build_script.bash -v /opt/mambaforge/envs/bioconda/conda-bld/:/opt/host-conda-bld -v /home/circleci/project/recipes/nextclade:/opt/recipe -e LANG=C.UTF-8 -e HOST_USER_ID=1001 quay.io/bioconda/bioconda-utils-build-env-cos7-aarch64 /bin/bash /opt/build_script.bash

https://app.circleci.com/pipelines/github/bioconda/bioconda-recipes/109939/workflows/d6e1d687-5cdc-4c5d-865a-1ba0cb41b932/jobs/180788/parallel-runs/0/steps/0-107

Need to run from source? but why is the aarch glibc version lower than linux-64? see conda-forge/tensorflow-feedstock#6

[corneliusroemer]

Skipping tests for aarch64 works - but isn't really super comforting - would be good to have a way of testing with current builder. See #46186

[rpetit3]

@corneliusroemer is the issue here that the prebuilt binaries are built with the newer GLIBC?

[corneliusroemer]

Yes, Rust has raised minimum glibc version to something like 2.17 from 1.64 - and the builder has a very old glibc, see #46186

As the glibc used is the one at runtime not on the builder and all runtimes will have sufficiently recent glibc versions for nextclade to work I'd say we just bypass tests until there's a better way.

what's strange is that tests run on x86 but not on aarch64 - there might be a slight difference been builders, again see #46186

I actually have quite an urgent use case for aarch64 bioconda nextclade so it'd be great if you could approve

[corneliusroemer]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Azure

No artifacts found on the most recent Azure build. Either the build failed, the artifacts have been removed due to age, or the recipe was blacklisted/skipped.

[corneliusroemer]

I've tried to work around the glibc issue but to no avail, see #46186 (comment)

Given the precedent quoted there for disabling tests when glibc causes issues (tensorflow etc.) I would like to ask for approval to skip tests just for the aarch version here.

[corneliusroemer]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Azure

Package(s) built on Azure are ready for inspection:

Arch	Package	Zip File
linux-64	nextclade-3.3.1-h9ee0642_1.tar.bz2	LinuxArtifacts

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You may also use conda to install these after downloading and extracting the appropriate zip file. From the LinuxArtifacts or OSXArtifacts directories:

conda install -c ./packages <package name>

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Docker image(s) built (images for Azure are in the LinuxArtifacts zip file above):

Package	Tag	Install with docker
nextclade	3.3.1--h9ee0642_1	show gzip -dc LinuxArtifacts/images/nextclade:3.3.1--h9ee0642_1.tar.gz | docker load

CircleCI

Package(s) built on CircleCI are ready for inspection:

Arch	Package	Repodata
linux-aarch64	nextclade-3.3.1-h23ed54d_1.tar.bz2	repodata.json

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You may also use conda to install these:

conda install -c https://output.circle-artifacts.com/output/job/73835433-b7cc-40de-b7c0-dbe96c478fe2/artifacts/0/tmp/artifacts/packages <package name>

[corneliusroemer]

I manually tested the aarch64 package in an aarch docker container (the one for create-env) and things work. So I think we're good to approve merge.

(base) root@e82e9469dc8e:/# file /opt/create-env/bin/nextclade
/opt/create-env/bin/nextclade: ELF 64-bit LSB pie executable, ARM aarch64, version 1 (SYSV), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, BuildID[sha1]=f774b66dc0f8781730fe9d8e02c2de25c4169bbc, stripped
(base) root@e82e9469dc8e:/# nextclade -h
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement.

Usage: nextclade [OPTIONS] <COMMAND>

Commands:
  completions      Generate shell completions
  run              Run sequence analysis: alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
  dataset          List and download available Nextclade datasets (pathogens)
  sort             Sort sequences according to the inferred Nextclade dataset (pathogen)
  read-annotation  Read genome annotation and present it in Nextclade's internal formats. This is mostly only useful for Nextclade maintainers and the most curious users. Note that these internal formats have no stability guarantees and can be changed at any time without notice
  help-markdown    Print command-line reference documentation in Markdown format
  help             Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help (see more with '--help')
  -V, --version  Print version

Verbosity:
      --verbosity <VERBOSITY>  Set verbosity level of console output [default: warn] [possible values: off, error, warn, info, debug, trace]
      --silent                 Disable all console output. Same as `--verbosity=off`
  -v, --verbose...             Make console output more verbose. Add multiple occurrences to increase verbosity further
  -q, --quiet...               Make console output more quiet. Add multiple occurrences to make output even more quiet

[corneliusroemer]

@BiocondaBot please add label