meryl: add linux-aarch64 and osx-arm64 build

[martin-g]

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[coderabbitai]

📝 Walkthrough

📝 Walkthrough

Walkthrough

The pull request introduces modifications to two files: build.sh and meta.yaml within the recipes/meryl directory. In build.sh, the command set -xe has been added at the beginning of the script. This command configuration ensures that the script will terminate immediately if any command fails and will print each command before its execution. A new variable ARCH_BUILD has been defined to include default flags for 64-bit architecture and SSE4.1 support, with adjustments for ARM architectures. The make command has been updated to utilize ARCH_BUILD in the CXXFLAGS, alongside the -Wno-c++20-extensions flag while maintaining the optimization flag -O3.

In meta.yaml, the version has been updated from 1.4.0 to 1.4.1, and the build number has been incremented from 0 to 1. The patches section now includes a comment indicating that the first patch is specific to macOS, and a new patch entry for 0003-align.patch has been added for ARM architectures. The extra section has been modified to include additional-platforms, specifying support for both linux-aarch64 and osx-arm64. No other significant changes have been made to the logic or structure of the file.

Possibly related PRs

• bambamc: add aarch64/arm64 builds #51067: The changes in build.sh for bambamc include the addition of set -xe, which is similar to the changes made in the main PR's build.sh, indicating a focus on error handling and debugging.
• metacache: add linux-aarch64 build #51106: The build.sh for metacache also includes the set -xe command, aligning with the changes in the main PR that enhance debugging and error handling.
• pydustmasker: add aarch64 build #51158: The build.sh for pydustmasker introduces environment variable exports for linker settings specific to ARM architectures, which relates to the ARM architecture considerations in the main PR.
• mashmap: add aarch64 build #51161: The build.sh for mashmap includes set -xe, similar to the main PR, indicating a focus on debugging and error handling.
• added arm and aarch64 builds #51184: The meta.yaml for mbgc adds support for linux-aarch64, which is relevant to the ARM architecture changes in the main PR.
• r-cobrar: add aarch64/arm64 builds #51203: The meta.yaml for r-cobrar adds support for linux-aarch64, aligning with the ARM architecture focus of the main PR.
• kmc: add arm64 build #51281: The meta.yaml for kmc adds support for osx-arm64, which is relevant to the changes in the main PR regarding ARM architecture.
• devider: add aarch64/arm64 builds #51370: The build.sh for devider includes architecture-specific modifications, which relate to the ARM architecture considerations in the main PR.
• vcf-validator: add linux-aarch64 build #51425: The meta.yaml for vcf-validator adds support for linux-aarch64, which is relevant to the architecture updates in the main PR.
• pybbi: add linux-aarch64 build #51516: The meta.yaml for pybbi adds support for linux-aarch64, aligning with the architecture changes in the main PR.
• centrifuge-core: add linux-aarch64 build #51517: The build.sh for centrifuge-core includes architecture-specific compilation flags, which relate to the ARM architecture considerations in the main PR.
• genodsp: add linux-aarch64 build #51597: The meta.yaml for genodsp adds support for linux-aarch64, which is relevant to the architecture updates in the main PR.
• d4binding: add aarch64/arm64 builds #51598: The meta.yaml for d4binding adds support for linux-aarch64, aligning with the changes in the main PR.
• psmc: add aarch64/arm64 builds #52230: The meta.yaml for psmc adds support for linux-aarch64, which is relevant to the main PR's focus on ARM architecture.
• relion: add aarch64/arm64 builds #52236: The meta.yaml for relion includes support for linux-aarch64, aligning with the changes in the main PR regarding ARM architecture.

Suggested labels

please review & merge, osx-arm64

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📥 Commits

Reviewing files that changed from the base of the PR and between cac22af and 48aad81.

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📥 Commits

Reviewing files that changed from the base of the PR and between cac22af and 48aad81.

📒 Files selected for processing (1)

• recipes/meryl/meta.yaml (2 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• recipes/meryl/meta.yaml

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[coderabbitai]

Actionable comments posted: 0

🧹 Outside diff range and nitpick comments (1)

recipes/meryl/build.sh (1)

3-4: LGTM! Good addition of build script safeguards.

Adding set -xe is a great practice for cross-architecture builds as it:

• Ensures immediate failure if any build step fails (-e)
• Provides verbose command logging (-x) which is valuable for debugging architecture-specific issues

📜 Review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between 25e1547 and 06850d7.

📒 Files selected for processing (2)

• recipes/meryl/build.sh (1 hunks)
• recipes/meryl/meta.yaml (2 hunks)

🔇 Additional comments (3)

recipes/meryl/meta.yaml (3)

13-13: LGTM! Appropriate platform selector added

The OSX selector # [osx] correctly specifies that this patch is macOS-specific, which matches its purpose of handling Clang on macOS.

---

17-17: LGTM! Appropriate build number increment

Build number increment is correct for adding new platform support. The presence of run_exports section helps maintain ABI compatibility across builds.

---

45-46: LGTM! Platform addition looks correct

The addition of linux-aarch64 to additional-platforms is properly configured. However, please verify that no additional platform-specific build or host requirements are needed for aarch64 support.

[mencian]

@BiocondaBot please fetch artifacts

[BiocondaBot]

Package(s) built are ready for inspection:

Arch	Package	Zip File / Repodata	CI	Instructions
linux-64	meryl-1.4.1-h4ac6f70_1.tar.bz2	linux-64.zip	GitHub Actions	show You may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>
osx-64	meryl-1.4.1-h79b9f80_1.tar.bz2	osx-64.zip	GitHub Actions	show You may also use conda to install after downloading and extracting the zip file. conda install -c ./packages <package name>
osx-arm64	meryl-1.4.1-h025cef0_1.tar.bz2	repodata.json	CircleCI	show You may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/596d6e64-e9f0-49e3-b346-3a7f371eff9e/artifacts/0/tmp/artifacts/packages <package name>
linux-aarch64	meryl-1.4.1-h78569d1_1.tar.bz2	repodata.json	CircleCI	show You may also use conda to install:conda install -c https://output.circle-artifacts.com/output/job/d1359d63-250f-41fd-8b6c-12af6568f39c/artifacts/0/tmp/artifacts/packages <package name>

---

Docker image(s) built:

Package	Tag	CI	Install with docker
meryl	1.4.1--h4ac6f70_1	GitHub Actions	show Images are in the linux-64 zip file above.gzip -dc images/meryl---1.4.1--h4ac6f70_1.tar.gz | docker load

[martin-g]

mgrigorov in 🌐 euler-arm-22 in /tmp/merrr via 🅒 test123 took 7s 
❯ tar xvf meryl-1.4.1-h78569d1_1.tar.bz2                                                                                                                                                                   (test123) 
info/run_exports.json
info/files
info/hash_input.json
info/test/run_test.sh
info/index.json
info/recipe/0002-macos-cmath.patch
info/recipe/build.sh
info/recipe/0003-align.patch
info/git
info/recipe/0001-Do-not-bail-out-for-Clang-on-macOS.patch
info/recipe/README.licenses
info/paths.json
info/recipe/meta.yaml.template
info/recipe/meta.yaml
info/recipe/conda_build_config.yaml
info/about.json
info/recipe/meryl-utility-aarch64.patch
bin/meryl-simple
bin/meryl-analyze
bin/meryl-import
bin/position-lookup
bin/meryl-lookup
bin/meryl
lib/libmeryl.a

mgrigorov in 🌐 euler-arm-22 in /tmp/merrr via 🅒 test123 
❯ file bin/*                                                                                                                                                                                               (test123) 
bin/meryl:           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/meryl-analyze:   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, not stripped
bin/meryl-import:    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, not stripped
bin/meryl-lookup:    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/meryl-simple:    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, not stripped
bin/position-lookup: 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

mgrigorov in 🌐 euler-arm-22 in /tmp/merrr via 🅒 test123 
❯ ./bin/meryl                                                                                                                                                                                              (test123) 
usage: ./bin/meryl ...

  A meryl command line is formed as a series of commands and files, possibly
  grouped using square brackets.  Each command operates on the file(s) that
  are listed after it.

  COMMANDS:

    statistics           display total, unique, distinct, present number of the kmers on the screen.  accepts exactly one input.
    histogram            display kmer frequency on the screen as 'frequency<tab>count'.  accepts exactly one input.
    print                display kmers on the screen as 'kmer<tab>count'.  accepts exactly one input.

    count                Count the occurrences of canonical kmers in the input.  must have 'output' specified.
    count-forward        Count the occurrences of forward kmers in the input.  must have 'output' specified.
    count-reverse        Count the occurrences of reverse kmers in the input.  must have 'output' specified.
      k=<K>              create mers of size K bases (mandatory).
      n=<N>              expect N mers in the input (optional; for precise memory sizing).
      memory=M           use no more than (about) M GB memory.
      threads=T          use no more than T threads.
      compress           compress homopolymer runs to a single letter.

    less-than N          return kmers that occur fewer than N times in the input.  accepts exactly one input.
    greater-than N       return kmers that occur more than N times in the input.  accepts exactly one input.
    equal-to N           return kmers that occur exactly N times in the input.  accepts exactly one input.
    not-equal-to N       return kmers that do not occur exactly N times in the input.  accepts exactly one input.

    increase X           add X to the count of each kmer.
    decrease X           subtract X from the count of each kmer.
    multiply X           multiply the count of each kmer by X.
    divide X             divide the count of each kmer by X.
    divide-round X       divide the count of each kmer by X and round results. count < X will become 1.
    modulo X             set the count of each kmer to the remainder of the count divided by X.

    union                return kmers that occur in any input, set the count to the number of inputs with this kmer.
    union-min            return kmers that occur in any input, set the count to the minimum count
    union-max            return kmers that occur in any input, set the count to the maximum count
    union-sum            return kmers that occur in any input, set the count to the sum of the counts

    intersect            return kmers that occur in all inputs, set the count to the count in the first input.
    intersect-min        return kmers that occur in all inputs, set the count to the minimum count.
    intersect-max        return kmers that occur in all inputs, set the count to the maximum count.
    intersect-sum        return kmers that occur in all inputs, set the count to the sum of the counts.

    subtract             return kmers that occur in the first input, substracting counts from the other inputs

    difference           return kmers that occur in the first input, but none of the other inputs
    symmetric-difference return kmers that occur in exactly one input

  MODIFIERS:

    output O             write kmers generated by the present command to an output  meryl database O
                         mandatory for count operations.

  EXAMPLES:

  Example:  Report 22-mers present in at least one of input1.fasta and input2.fasta.
            Kmers from each input are saved in meryl databases 'input1' and 'input2',
            but the kmers in the union are only reported to the screen.

            meryl print \
                    union \
                      [count k=22 input1.fasta output input1] \
                      [count k=22 input2.fasta output input2]

  Example:  Find the highest count of each kmer present in both files, save the kmers to
            database 'maxCount'.

            meryl intersect-max input1 input2 output maxCount

  Example:  Find unique kmers common to both files.  Brackets are necessary
            on the first 'equal-to' command to prevent the second 'equal-to' from
            being used as an input to the first 'equal-to'.

            meryl intersect [equal-to 1 input1] equal-to 1 input2

LGTM!

[martin-g]

@BiocondaBot please add label

[martin-g]

Thank you for the help, @mencian !