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meraculous: add linux-aarch64 build #50566

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@martin-g martin-g commented Sep 9, 2024

Describe your pull request here


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@martin-g martin-g added the aarch64 Related to adding linux-aarch64 support label Sep 9, 2024
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martin-g commented Sep 9, 2024

The Linux ARM64 build depends on missing conda-forge/perl-dbi package

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The Linux ARM64 build depends on missing conda-forge/perl-dbi package:

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coderabbitai bot commented Nov 20, 2024

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Walkthrough

The pull request introduces modifications to two files: build.sh and meta.yaml in the meraculous package. In build.sh, the command set -xe is added at the beginning to ensure the script exits upon encountering errors and prints each command before execution. Additionally, the make command is updated to include the -j ${CPU_COUNT} option, enabling parallel compilation based on the available CPU cores. In meta.yaml, the package version is updated from "2.2.5" to "2.2.6", and the build number is incremented from 7 to 8. A new entry for run_exports is added, which includes a pinning directive for the meraculous subpackage. Furthermore, a new key additional-platforms is introduced in the extra section to specify support for the linux-aarch64 platform. No changes were made to the existing requirements, source, test commands, or the about section.

Possibly related PRs

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osx-arm64

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Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)
recipes/meraculous/meta.yaml (1)

Line range hint 22-35: Add missing perl-dbi dependency

Based on the PR comments, this package requires perl-dbi, but it's not listed in the requirements section. Please add it to both host and run requirements once the conda-forge/perl-dbi-feedstock PR is merged.

  host:
    - libgd >=2.0
    - boost-cpp
    - perl
    - perl-log-log4perl >=1.31
    - gnuplot >=3.7
+   - perl-dbi
  run:
    - libgd >=2.0
    - boost-cpp
    - perl
    - perl-log-log4perl >=1.31
    - gnuplot >=3.7
+   - perl-dbi
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📒 Files selected for processing (2)
  • recipes/meraculous/build.sh (1 hunks)
  • recipes/meraculous/meta.yaml (2 hunks)
🔇 Additional comments (4)
recipes/meraculous/build.sh (2)

3-4: LGTM! Enhanced error handling and debugging

Adding set -xe is a good practice that will help catch build failures early and provide better debugging information, especially important for the new ARM64 platform support.


11-11: LGTM! Optimized build performance

The addition of parallel compilation with -j ${CPU_COUNT} is a good optimization that follows Conda build best practices.

recipes/meraculous/meta.yaml (2)

16-18: LGTM! Good addition of run_exports.

The addition of run_exports with appropriate pinning will help maintain ABI compatibility for downstream packages.


56-57: Verify all dependencies for linux-aarch64

While adding linux-aarch64 support, please ensure all dependencies are available for this architecture. Currently, there's a known issue with the perl-dbi package.

Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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Package(s) built are ready for inspection:

Arch Package Zip File / Repodata CI Instructions
linux-64 meraculous-2.2.6-pl5321h4ac6f70_8.tar.bz2 linux-64.zip GitHub Actions
showYou may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>
linux-aarch64 meraculous-2.2.6-pl5321h78569d1_8.tar.bz2 repodata.json CircleCI
showYou may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/9c181fcc-a9e6-458a-8041-ce36d2eeaf32/artifacts/0/tmp/artifacts/packages <package name>

Docker image(s) built:

Package Tag CI Install with docker
meraculous 2.2.6--pl5321h4ac6f70_8 GitHub Actions
showImages are in the linux-64 zip file above.gzip -dc images/meraculous---2.2.6--pl5321h4ac6f70_8.tar.gz | docker load

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mgrigorov in 🌐 euler-arm-22 in /tmp/hhh via 🅒 test123 took 1m33s 
❯ tar xvf meraculous-2.2.6-pl5321h78569d1_8.tar.bz2                                                                                                                                                        (test123) 
info/run_exports.json
info/test/run_test.sh
info/recipe/build.sh
info/hash_input.json
info/index.json
info/recipe/meraculous-aarch64.patch
info/recipe/0001-Remove-compiler-upper-bound-version-check.patch
info/has_prefix
info/recipe/0002-No-static-linking.patch
info/recipe/meta.yaml.template
info/files
info/licenses/license.txt
info/recipe/conda_build_config.yaml
info/recipe/meta.yaml
info/about.json
info/paths.json
info/git
etc/meraculous/merBlast/temp.2
etc/meraculous/meraculous.local.params.defs
etc/meraculous/meraculous.params.defs
bin/test_dependencies.pl
bin/randomList2.pl
bin/divide_it.pl
bin/scaffold2contig.pl
bin/unique.pl
bin/fasta_splitter.pl
bin/contigBias.pl
bin/N50.pl
bin/optimize2.pl
bin/kmerHistAnalyzer.pl
bin/screen_list2.pl
bin/findDMin2.pl
bin/bubbleScout.pl
bin/histogram2.pl
bin/loadBalanceMers.pl
etc/meraculous/merBlast/bv3Diff.pl
bin/gapDivider.pl
bin/scaffReportToFasta.pl
bin/splinter.pl
bin/haplotyper.Naive.pl
bin/split_and_validate_reads.pl
bin/haplotyper.pl
bin/spanner.pl
bin/splinter_scaffolds.pl
bin/bmaToLinks.pl
bin/blastMapAnalyzer2.pl
bin/gapPlacer.pl
bin/meraculous4h.pl
bin/_bubbleFinder2.pl
bin/bubblePopper.pl
bin/_oNo4.pl
bin/oNo7.pl
bin/meraculous.pl
legal.txt
license.txt
share/doc/meraculous/Intermediate_outputs.txt
etc/meraculous/merBlast/ECO.1Mish.sample
etc/meraculous/pipeline/jumps.fastq.25K
etc/meraculous/pipeline/frags.fastq.25K
etc/meraculous/merBlast/ECO.1Mish.sample.info
etc/meraculous/merBlast/merBlast.unitTest.reads.info
etc/meraculous/merBlast/temp
share/doc/meraculous/meraculous.config.template
etc/meraculous/merBlast/merBlast.unitTest.reads
etc/meraculous/merBlast/ECO.1Mish.blastall.bv3
etc/meraculous/merBlast/ECO.1Mish.merBlast.bv3
bin/memtime
bin/merauder
bin/mergeMerBlasts
bin/fasta_stats
bin/contigMerDepth_128mer
bin/contigMerDepth_56mer
bin/meraculousTh_56mer
bin/meraculousTh_128mer
bin/merBlast_128mer
bin/merBlast_56mer
bin/merCounterTh_56mer
bin/merCounterTh_128mer
bin/mergraphTh_128mer
bin/mergraphTh_56mer
bin/UnitTest_LV
etc/meraculous/merBlast/ECO.contigs.fa
README.md
lib/M_LibData.pm
lib/M_Constants.pm
lib/M_Utility.pm
lib/M_Generic_Config.pm
lib/M_Job_Set.pm
etc/meraculous/merBlast/merBlast.unitTest.result.ref
etc/meraculous/pipeline/meraculous.config
etc/meraculous/merBlast/merBlast.unitTest.contigs
share/doc/meraculous/Manual.pdf
bin/run_meraculous.sh
test_install.sh
bin/bootstrap_run.sh
bin/isjobcomplete.sh
bin/cluster_submit.sh
bin/evaluate_meraculous_run.sh

mgrigorov in 🌐 euler-arm-22 in /tmp/hhh via 🅒 test123 took 20s 
❯ file bin/*                                                                                                                                                                                               (test123) 
bin/_bubbleFinder2.pl:           Perl script text executable
bin/_oNo4.pl:                    Perl script text executable
bin/blastMapAnalyzer2.pl:        Perl script text executable
bin/bmaToLinks.pl:               Perl script text executable
bin/bootstrap_run.sh:            Bourne-Again shell script, ASCII text executable
bin/bubblePopper.pl:             Perl script text executable
bin/bubbleScout.pl:              Perl script text executable
bin/cluster_submit.sh:           Bourne-Again shell script, ASCII text executable
bin/contigBias.pl:               Perl script text executable
bin/contigMerDepth_56mer:        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/contigMerDepth_128mer:       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/divide_it.pl:                Perl script text executable
bin/evaluate_meraculous_run.sh:  Bourne-Again shell script, ASCII text executable
bin/fasta_splitter.pl:           Perl script text executable
bin/fasta_stats:                 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/findDMin2.pl:                Perl script text executable
bin/gapDivider.pl:               Perl script text executable
bin/gapPlacer.pl:                Perl script text executable
bin/haplotyper.Naive.pl:         Perl script text executable
bin/haplotyper.pl:               Perl script text executable
bin/histogram2.pl:               Perl script text executable
bin/isjobcomplete.sh:            Bourne-Again shell script, ASCII text executable
bin/kmerHistAnalyzer.pl:         Perl script text executable
bin/loadBalanceMers.pl:          Perl script text executable
bin/memtime:                     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/meraculous.pl:               Perl script text executable
bin/meraculous4h.pl:             Perl script text executable
bin/meraculousTh_56mer:          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/meraculousTh_128mer:         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/merauder:                    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/merBlast_56mer:              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/merBlast_128mer:             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/merCounterTh_56mer:          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/merCounterTh_128mer:         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/mergeMerBlasts:              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/mergraphTh_56mer:            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/mergraphTh_128mer:           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/N50.pl:                      Perl script text executable
bin/oNo7.pl:                     Perl script text executable
bin/optimize2.pl:                Perl script text executable
bin/randomList2.pl:              Perl script text executable
bin/run_meraculous.sh:           Bourne-Again shell script, ASCII text executable
bin/scaffold2contig.pl:          Perl script text executable
bin/scaffReportToFasta.pl:       Perl script text executable
bin/screen_list2.pl:             Perl script text executable
bin/spanner.pl:                  Perl script text executable
bin/splinter.pl:                 Perl script text executable
bin/splinter_scaffolds.pl:       Perl script text executable
bin/split_and_validate_reads.pl: Perl script text executable
bin/test_dependencies.pl:        Perl script text executable
bin/unique.pl:                   Perl script text executable
bin/UnitTest_LV:                 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 

mgrigorov in 🌐 euler-arm-22 in /tmp/hhh via 🅒 test123 
❯ ./bin/merauder --help                                                                                                                                                                                    (test123) 
Usage: merauder [OPTION...] 
Options:

  -A                         Aggressive closures
  -c char*                   Contig FASTA file
  -D int                     Minimum depth (default 2)
  -g char*                   Gap data file
  -i int                     Maximum insert size
  -m int                     Mer size
  -P                         Polymorphic mode
  -Q int                     Quality offset (default 33)
  -R double                  Exclude repeats
  -s char*                   Scaffold report file
  -V                         Verbose mode
  -?, --help                 Give this help list
      --usage                Give a short usage message
      --version              Print program version

LGTM!

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@BiocondaBot please add label

@BiocondaBot BiocondaBot added the please review & merge set to ask for merge label Nov 25, 2024
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