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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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zol: add aarch64/arm64 builds #51711

Open martin-g opened 3 days ago

martin-g commented 3 days ago

Describe your pull request here

Please read the guidelines for Bioconda recipes before opening a pull request (PR).

General instructions

Instructions for avoiding API, ABI, and CLI breakage issues

Conda is able to record and lock (a.k.a. pin) dependency versions used at build time of other recipes. This way, one can avoid that expectations of a downstream recipe with regards to API, ABI, or CLI are violated by later changes in the recipe. If not already present in the meta.yaml, make sure to specify run_exports (see here for the rationale and comprehensive explanation). Add a run_exports section like this:

build:
  run_exports:
    - ...

with ... being one of:

Case run_exports statement
semantic versioning {{ pin_subpackage("myrecipe", max_pin="x") }}
semantic versioning (0.x.x) {{ pin_subpackage("myrecipe", max_pin="x.x") }}
known breakage in minor versions {{ pin_subpackage("myrecipe", max_pin="x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
known breakage in patch versions {{ pin_subpackage("myrecipe", max_pin="x.x.x") }} (in such a case, please add a note that shortly mentions your evidence for that)
calendar versioning {{ pin_subpackage("myrecipe", max_pin=None) }}

while replacing "myrecipe" with either name if a name|lower variable is defined in your recipe or with the lowercase name of the package in quotes.

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coderabbitai[bot] commented 3 days ago
📝 Walkthrough
📝 Walkthrough ## Walkthrough The pull request introduces modifications to the `build.sh` script and the `meta.yaml` files for the `zol`, `miniprot`, and `prodigal-gv` packages. In each `build.sh`, the command `set -xe` has been added to facilitate immediate script termination upon command failure and to enhance command visibility during execution. The `miniprot` and `prodigal-gv` scripts also incorporate the `-j"${CPU_COUNT}"` option in their `make` commands for parallel compilation. The overall structure and functionality of the scripts remain consistent, focusing on directory creation and file management. In the `meta.yaml` files, the build number is incremented in each package, and support for additional platforms, specifically `linux-aarch64` and `osx-arm64`, has been introduced under the `extra` section for all three packages. The existing dependencies and test commands remain unchanged, ensuring that the core functionality of the packages is preserved while expanding their compatibility. ## Possibly related PRs - **#49740**: The `build.sh` script for `kmer-db` was modified to include `set -xe`, similar to the changes made in the main PR, enhancing error handling and debugging. - **#50103**: The `meta.yaml` file for `tracs` was updated to include `additional-platforms` for `linux-aarch64` and `osx-arm64`, which aligns with the changes in the main PR that also added support for these architectures. - **#50996**: The `meta.yaml` for `tRNAscan-SE` includes `additional-platforms` for `linux-aarch64` and `osx-arm64`, reflecting similar updates made in the main PR. - **#51067**: The `build.sh` for `bambamc` was updated to include `set -xe`, enhancing error handling, which is consistent with the changes in the main PR. - **#51105**: The `meta.yaml` for `pyslow5` was modified to add `additional-platforms`, aligning with the main PR's updates. - **#51106**: The `meta.yaml` for `metacache` added support for `linux-aarch64`, similar to the main PR's changes. - **#51121**: The `meta.yaml` for `longreadsum` included `additional-platforms`, consistent with the main PR's modifications. - **#51124**: The `meta.yaml` for `phables` was updated to include `additional-platforms`, reflecting the changes in the main PR. - **#51161**: The `build.sh` for `mashmap` was modified to include `set -xe`, similar to the main PR's changes. - **#51203**: The `meta.yaml` for `r-cobrar` added `additional-platforms`, aligning with the main PR's updates. - **#51206**: The `meta.yaml` for `pepnovo` included `additional-platforms`, consistent with the main PR's changes. - **#51425**: The `meta.yaml` for `vcf-validator` added support for `linux-aarch64`, similar to the main PR's modifications. - **#51448**: The `meta.yaml` for `genbank` included `additional-platforms`, reflecting the changes made in the main PR. - **#51598**: The `meta.yaml` for `d4binding` added support for `linux-aarch64`, consistent with the main PR's updates. ## Suggested labels `please review & merge` ## Suggested reviewers - rpetit3 - mencian

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martin-g commented 3 days ago

The Linux ARM64 build fails due to:

Could not solve for environment specs
14:06:21 BIOCONDA INFO (OUT) The following packages are incompatible
14:06:21 BIOCONDA INFO (OUT) ├─ axel does not exist (perhaps a typo or a missing channel);
14:06:21 BIOCONDA INFO (OUT) ├─ miniprot 0.7.*  does not exist (perhaps a typo or a missing channel);
14:06:21 BIOCONDA INFO (OUT) └─ prodigal-gv does not exist (perhaps a typo or a missing channel).

PRs: