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cloudspades: add linux-aarch64 build #51446

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merged 3 commits into from
Oct 17, 2024

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Describe your pull request here


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Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
@martin-g martin-g added the aarch64 Related to adding linux-aarch64 support label Oct 17, 2024
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📝 Walkthrough
📝 Walkthrough

Walkthrough

The pull request modifies the meta.yaml file for the cloudspades package. The version number remains at 3.16.0, while the build number is incremented from 0 to 1. The source section is unchanged except for corrected indentation. A new entry is added to the extra section, specifying additional-platforms with the value linux-aarch64. Additionally, the indentation of the doc_url line is corrected. There are no modifications to the requirements or test commands in this update. The build.sh script is also updated to include an additional flag in the CXXFLAGS environment variable, appending -fsigned-char to the existing flags, which alters the compilation settings for C++ files. The CircleCI configuration file .circleci/config.yml is updated to increase the resource class for the linux-aarch64 executor from arm.medium to arm.large, and various job definitions are refined to accommodate builds on the specified platforms.

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Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
.circleci/config.yml (1)

Line range hint 1-385: Overall configuration review: ARM support looks comprehensive

The CircleCI configuration for ARM support (both osx-arm64 and linux-aarch64) appears comprehensive and well-structured. It covers various scenarios including PR builds, master branch builds, bulk builds, and nightly builds. The separation of concerns between different job types is commendable.

Consider the following suggestions for further improvements:

  1. Caching: Implement caching strategies for dependencies to speed up builds.
  2. Parallelization: Explore opportunities to parallelize steps within jobs where possible.
  3. Conditional Execution: Implement more granular conditional execution to skip unnecessary steps based on the changes in a PR.
  4. Error Handling: Enhance error handling and reporting, especially for the bulk and nightly builds.
  5. Documentation: Add inline comments explaining the purpose of critical or complex steps.

To verify the effectiveness of the current configuration, you can run the following script to analyze job success rates:

#!/bin/bash
# Description: Analyze job success rates for ARM builds

# Note: Ensure you have the CircleCI CLI installed and configured

# Function to get success rate for a job
get_success_rate() {
  local job_name=$1
  local total=$(circleci job list bioconda/bioconda-recipes --filter "$job_name" --limit 100 | jq '.total_items')
  local success=$(circleci job list bioconda/bioconda-recipes --filter "$job_name" --limit 100 | jq '.items[] | select(.status == "success") | .id' | wc -l)
  echo "scale=2; $success / $total * 100" | bc
}

echo "Success rates for ARM builds:"
echo "build_and_test (osx-arm64): $(get_success_rate 'build_and_test-osx-arm64')%"
echo "build_and_test (linux-aarch64): $(get_success_rate 'build_and_test-linux-aarch64')%"
echo "build_and_upload (osx-arm64): $(get_success_rate 'build_and_upload-osx-arm64')%"
echo "build_and_upload (linux-aarch64): $(get_success_rate 'build_and_upload-linux-aarch64')%"
echo "bulk_build (linux-aarch64): $(get_success_rate 'bulk_build-linux-aarch64')%"
echo "nightly_build (linux-aarch64): $(get_success_rate 'nightly_build-linux-aarch64')%"

This script will help identify any jobs that may need attention due to low success rates.

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Files that changed from the base of the PR and between cafa0cf and 6820164.

📒 Files selected for processing (1)
  • .circleci/config.yml (1 hunks)
🧰 Additional context used
🔇 Additional comments (1)
.circleci/config.yml (1)

12-12: Approved: Increased resource class for linux-aarch64 executor

The change from arm.medium to arm.large for the linux-aarch64 executor is appropriate for supporting the new ARM64 build. This should provide more resources for potentially resource-intensive builds.

To ensure this change is beneficial:

  1. Monitor build times and success rates for linux-aarch64 builds after this change.
  2. Compare resource utilization between arm.medium and arm.large to justify the increased cost.

Run the following script to check recent build times for linux-aarch64:

This will help in assessing the impact of the resource class change on build performance.

@martin-g
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@BiocondaBot please fetch artifacts

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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 cloudspades-3.16.0-h6dccd9a_1.tar.bz2 LinuxArtifacts.zip Azure
showYou may also use conda to install after downloading and extracting the zip file. From the LinuxArtifacts directory: conda install -c ./packages <package name>
linux-aarch64 cloudspades-3.16.0-hf9a8d21_1.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/f1592535-18b2-475c-8caf-499a7d4b2b40/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
cloudspades 3.16.0--h6dccd9a_1 Azure
showImages for Azure are in the LinuxArtifacts zip file above.gzip -dc LinuxArtifacts/images/cloudspades:3.16.0--h6dccd9a_1.tar.gz | docker load

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mgrigorov in 🌐 euler-arm-22 in /tmp/cloudspades via 🅒 test123 took 40s 
❯ tar xvf cloudspades-3.16.0-hf9a8d21_1.tar.bz2                                                                                                                                                            (test123) 
info/run_exports.json
info/hash_input.json
info/test/run_test.sh
info/index.json
info/recipe/build.sh
info/recipe/meta.yaml.template
info/recipe/0001-change-verbosity-remove-expr.patch
info/licenses/assembler/LICENSE
info/recipe/meta.yaml
info/files
info/recipe/conda_build_config.yaml
info/about.json
info/paths.json
info/git
share/spades/sewage/usher_barcodes.csv
share/spades/rnaspades_manual.html
share/spades/manual.html
bin/rnaviralspades.py
bin/plasmidspades.py
bin/metaspades.py
bin/metaplasmidspades.py
bin/coronaspades.py
bin/rnaspades.py
bin/metaviralspades.py
share/spades/joblib3/_compat.py
share/spades/joblib3/testing.py
share/spades/spades_pipeline/executors/executors.py
share/spades/spades_pipeline/scripts/copy_files.py
share/spades/spades_pipeline/stages/stage.py
share/spades/spades_pipeline/executors/executor_save_yaml.py
share/spades/spades_pipeline/scripts/plasmid_glue.py
share/spades/pyyaml3/loader.py
share/spades/joblib3/_multiprocessing_helpers.py
share/spades/spades_pipeline/stages/terminating_stage.py
share/spades/pyyaml3/nodes.py
share/spades/spades_pipeline/stages/pipeline.py
share/spades/spades_pipeline/stages/breaking_scaffolds_stage.py
bin/spades_init.py
share/spades/spades_pipeline/stages/before_start_stage.py
share/spades/spades_pipeline/stages/check_test_stage.py
share/spades/spades_pipeline/stages/scaffold_correction_stage.py
share/spades/spades_pipeline/scripts/breaking_scaffolds_script.py
share/spades/spades_pipeline/commands_parser.py
share/spades/spades_pipeline/common/parallel_launcher.py
share/spades/pyyaml3/events.py
share/spades/spades_pipeline/scripts/preprocess_contigs.py
share/spades/pyyaml3/error.py
share/spades/pyyaml3/tokens.py
share/spades/pyyaml3/dumper.py
share/spades/spades_pipeline/common/alignment.py
share/spades/spades_pipeline/executors/executor_local.py
share/spades/joblib3/my_exceptions.py
share/spades/joblib3/disk.py
share/spades/pyyaml3/cyaml.py
share/spades/spades_pipeline/scripts/correction_iteration_script.py
share/spades/spades_pipeline/scripts/check_test_script.py
share/spades/joblib3/_memory_helpers.py
share/spades/spades_pipeline/options_storage.py
share/spades/pyyaml3/serializer.py
share/spades/spades_pipeline/scripts/preprocess_interlaced_reads.py
share/spades/spades_pipeline/process_cfg.py
share/spades/joblib3/__init__.py
share/spades/spades_pipeline/scripts/compress_all.py
share/spades/pyyaml3/composer.py
share/spades/joblib3/logger.py
share/spades/spades_pipeline/common/SeqIO.py
share/spades/spades_pipeline/stages/correction_stage.py
share/spades/pyyaml3/reader.py
share/spades/spades_pipeline/stages/spades_iteration_stage.py
share/spades/pyyaml3/resolver.py
share/spades/spades_pipeline/common/sam_parser.py
share/spades/joblib3/hashing.py
share/spades/spades_pipeline/stages/error_correction_stage.py
share/spades/pyyaml3/__init__.py
share/spades/joblib3/func_inspect.py
share/spades/spades_pipeline/stages/preprocess_reads_stage.py
share/spades/pyyaml3/representer.py
share/spades/joblib3/format_stack.py
share/spades/joblib3/numpy_pickle.py
share/spades/spades_pipeline/stages/spades_stage.py
share/spades/joblib3/pool.py
share/spades/pyyaml3/parser.py
share/spades/pyyaml3/constructor.py
share/spades/spades_pipeline/support.py
bin/spades.py
share/spades/joblib3/parallel.py
share/spades/joblib3/memory.py
share/spades/pyyaml3/emitter.py
share/spades/pyyaml3/scanner.py
share/spades/spades_pipeline/options_parser.py
share/spades/spades_pipeline/common/__init__.py
share/spades/spades_pipeline/stages/__init__.py
share/spades/test_dataset/reference_1K.fa.gz
share/spades/biosynthetic_spades_hmms/KR.hmm.gz
share/spades/biosynthetic_spades_hmms/TE.hmm.gz
share/spades/biosynthetic_spades_hmms/CStart.hmm.gz
share/spades/biosynthetic_spades_hmms/AT.hmm.gz
share/spades/biosynthetic_spades_hmms/KS.hmm.gz
share/spades/biosynthetic_spades_hmms/AMP.hmm.gz
share/spades/test_dataset_plasmid/pl1.fq.gz
share/spades/test_dataset_plasmid/pl2.fq.gz
share/spades/test_dataset/ecoli_1K_1.fq.gz
share/spades/test_dataset/ecoli_1K_2.fq.gz
share/spades/coronaspades_hmms/Phan-CoV.hmm.gz
share/spades/coronaspades_hmms/Pfam-A.SARS-CoV-2.hmm.gz
share/spades/test_dataset/operons_1K.gff
share/spades/test_dataset/genes_1K.gff
share/spades/VERSION
share/spades/LICENSE
share/spades/README.md
bin/spades-bwa
bin/spades-convert-bin-to-fasta
bin/spades-corrector-core
bin/spades-hammer
bin/spades-kmercount
bin/spades-kmer-estimating
bin/spades-ionhammer
bin/spades-read-filter
bin/spades-gbuilder
bin/spades-gsimplifier
bin/spades-gmapper
filebin/spades-core
^[[Cshare/spades/configs/debruijn/toy.info
share/spades/configs/debruijn/isolate_mode.info
share/spades/configs/debruijn/metaplasmid_mode.info
share/spades/configs/debruijn/hmm_mode.info
share/spades/configs/debruijn/large_genome_mode.info
share/spades/configs/debruijn/tsa.info
share/spades/configs/corrector/corrector.info
share/spades/configs/debruijn/plasmid_mode.info
share/spades/configs/debruijn/careful_mda_mode.info
share/spades/configs/debruijn/careful_mode.info
share/spades/configs/debruijn/rnaviral_mode.info
share/spades/configs/debruijn/construction.info
share/spades/configs/debruijn/detail_info_printer.info
share/spades/configs/debruijn/metaviral_mode.info
share/spades/configs/debruijn/sewage_mode.info
share/spades/configs/hammer/config.info
share/spades/configs/debruijn/distance_estimation.info
share/spades/configs/debruijn/mda_mode.info
share/spades/configs/debruijn/meta_mode.info
share/spades/configs/debruijn/config.info
share/spades/configs/debruijn/rna_mode.info
share/spades/configs/debruijn/simplification.info
share/spades/configs/debruijn/pe_params.info
share/spades/configs/debruijn/tslr_resolver.info
share/spades/test_dataset/operons_1K.txt
share/spades/test_dataset/genes_1K.txt
share/spades/GPLv2.txt
share/spades/configs/ionhammer/ionhammer.cfg

mgrigorov in 🌐 euler-arm-22 in /tmp/cloudspades via 🅒 test123 took 7s 
❯ file bin/*                                                                                                                                                                                               (test123) 
bin/coronaspades.py:             symbolic link to spades.py
bin/metaplasmidspades.py:        symbolic link to spades.py
bin/metaspades.py:               symbolic link to spades.py
bin/metaviralspades.py:          symbolic link to spades.py
bin/plasmidspades.py:            symbolic link to spades.py
bin/rnaspades.py:                symbolic link to spades.py
bin/rnaviralspades.py:           symbolic link to spades.py
bin/spades-bwa:                  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, with debug_info, not stripped
bin/spades-convert-bin-to-fasta: ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades-core:                 ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades-corrector-core:       ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades-gbuilder:             ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades-gmapper:              ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades-gsimplifier:          ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades-hammer:               ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades-ionhammer:            ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades-kmer-estimating:      ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades-kmercount:            ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades-read-filter:          ELF 64-bit LSB pie executable, ARM aarch64, version 1 (GNU/Linux), dynamically linked, interpreter /lib/ld-linux-aarch64.so.1, for GNU/Linux 3.7.0, with debug_info, not stripped
bin/spades.py:                   Python script, ASCII text executable
bin/spades_init.py:              Python script, ASCII text executable

mgrigorov in 🌐 euler-arm-22 in /tmp/cloudspades via 🅒 test123 
❯ ./bin/spades-bwa                                                                                                                                                                                         (test123) 

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.16a-r1185-dirty
Contact: Heng Li <[email protected]>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         shm           manage indices in shared memory
         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         bwtupdate     update .bwt to the new format
         bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual.

LGTM!

@martin-g
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@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Oct 17, 2024
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