Add get_mnv #51178
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| {% set name = "get_mnv" %} | ||||||||
| {% set version = "1.0.0" %} | ||||||||
| {% set sha256 = "b9ba6fe1a5f5f73afa98cde9e348f7861d44690f795338816a8a0724a66e1aa8" %} | ||||||||
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| package: | ||||||||
| name: "{{ name|lower }}" | ||||||||
| version: "{{ version }}" | ||||||||
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| source: | ||||||||
| url: "https://github.com/PathoGenOmics-Lab/{{ name }}/archive/refs/tags/{{ version }}.tar.gz" | ||||||||
| sha256: "{{ sha256 }}" | ||||||||
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| build: | ||||||||
| number: 0 | ||||||||
| script: | | ||||||||
| export LANG=C.UTF-8 | ||||||||
| export LC_ALL=C.UTF-8 | ||||||||
| export RUST_BACKTRACE=1 | ||||||||
| export OPENSSL_NO_VENDOR=1 | ||||||||
| export OPENSSL_DIR=$PREFIX | ||||||||
| export OPENSSL_INCLUDE_DIR=$PREFIX/include | ||||||||
| export OPENSSL_LIB_DIR=$PREFIX/lib | ||||||||
| export CURL_STATIC_SSL=1 | ||||||||
| export CURL_SYS_STATIC=1 | ||||||||
| #export CARGO_NET_OFFLINE=true | ||||||||
| export HTS_LIB_DIR=$PREFIX/lib | ||||||||
| export HTS_INCLUDE_DIR=$PREFIX/include | ||||||||
| export HTS_STATIC=1 | ||||||||
| export HTS_SYS_BUNDLED=0 | ||||||||
| cargo install --no-track --locked --verbose --root "${PREFIX}" --path . | ||||||||
| run_exports: | ||||||||
| - {{ pin_subpackage(name, max_pin="x") }} | ||||||||
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| requirements: | ||||||||
| build: | ||||||||
| - {{ compiler('rust') }} | ||||||||
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| host: | ||||||||
| - openssl | ||||||||
| - curl | ||||||||
| - pkg-config | ||||||||
| - htslib | ||||||||
| - bzip2 | ||||||||
| - xz | ||||||||
| - zlib | ||||||||
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There was a problem hiding this comment. 🛠️ Refactor suggestion Add run section with pinned library versions. The requirements section is well-structured with build and host sections. However, it's missing a run section to specify runtime dependencies. Consider adding a run section with pinned versions of the libraries: run:
- {{ pin_compatible('openssl') }}
- {{ pin_compatible('curl') }}
- {{ pin_compatible('htslib') }}
- {{ pin_compatible('bzip2') }}
- {{ pin_compatible('xz') }}
- {{ pin_compatible('zlib') }}This ensures that the package uses compatible versions of the libraries at runtime. |
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| run: | ||||||||
| - {{ pin_compatible('openssl') }} | ||||||||
| - {{ pin_compatible('curl') }} | ||||||||
| - {{ pin_compatible('htslib') }} | ||||||||
| - {{ pin_compatible('bzip2') }} | ||||||||
| - {{ pin_compatible('xz') }} | ||||||||
| - {{ pin_compatible('zlib') }} | ||||||||
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| test: | ||||||||
| commands: | ||||||||
| - get_mnv --help | ||||||||
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There was a problem hiding this comment. 🛠️ Refactor suggestion Enhance test coverage. While the current test ensures that the test:
commands:
- get_mnv --help
- get_mnv --version
- get_mnv --test # If there's a built-in test option
# Add a command to run get_mnv on a small test dataset, if possibleThese additional tests would provide better assurance that the tool is functioning correctly after installation. Would you like assistance in generating more specific test commands based on the tool's functionality? |
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| - get_mnv --version | ||||||||
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| about: | ||||||||
| home: "https://github.com/PathoGenOmics-Lab/get_mnv" | ||||||||
| license: "GPL-3.0" | ||||||||
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Suggested change
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| license_family: GPL3 | ||||||||
| license_file: LICENSE | ||||||||
| summary: "Tool to identify Multi-Nucleotide Variants (MNVs) in genomic sequences." | ||||||||
| description: | | ||||||||
| get_MNV is a tool designed to identify Multi-Nucleotide Variants (MNVs) within the same codon in genomic sequences, providing more accurate annotation for genomic data. | ||||||||
| doc_url: "https://github.com/PathoGenOmics-Lab/get_mnv" | ||||||||
| dev_url: "https://github.com/PathoGenOmics-Lab/get_mnv" | ||||||||
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| extra: | ||||||||
| recipe-maintainers: | ||||||||
| - PathoGenOmics-Lab | ||||||||
| categories: | ||||||||
| - Genomics | ||||||||
| - Variant Analysis | ||||||||
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The libraries should be in 'host', not 'build'