Add vclust #50007
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| {% set version = "1.2.7" %} | ||
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| {% set system = "x64_linux" %} # [linux and x86_64] | ||
| {% set system = "x64_mac" %} # [osx and x86_64] | ||
| {% set system = "arm64_linux" %} # [linux and aarch64] | ||
| {% set system = "arm64_mac" %} # [osx and arm64] | ||
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| {% set sha256 = "5f750bd1bfc8448d127ea8a566860bc10c58c768a79d3d9a814243d64c1f16cf" %} # [linux and x86_64] | ||
| {% set sha256 = "077a44e14e429a526868ca16364c62b800eeade9aa7df184fdda8f93e053c356" %} # [osx and x86_64] | ||
| {% set sha256 = "9b2b410607d26ec05b1bdc42329b73285e4a862c93f67aff6c157b10b02e3383" %} # [linux and aarch64] | ||
| {% set sha256 = "b917c5af92e806b4244a62a32063c81bc9de3eae3760498444398fe7c5a7f623" %} # [osx and arm64] | ||
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| package: | ||
| name: vclust | ||
| version: {{ version }} | ||
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| build: | ||
| number: 0 | ||
| run_exports: | ||
| - {{ pin_subpackage('vclust', max_pin='x') }} | ||
| script: | | ||
| mkdir -p ${PREFIX}/bin | ||
| cp -r vclust.py bin ${PREFIX}/bin/ | ||
| chmod +x ${PREFIX}/bin/vclust.py | ||
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| source: | ||
| url: https://github.com/refresh-bio/vclust/releases/download/v{{ version }}/vclust-v{{ version }}-{{ system }}.tar.gz | ||
| sha256: {{ sha256 }} | ||
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| requirements: | ||
| host: | ||
| - python >=3.7 | ||
| run: | ||
| - python >=3.7 | ||
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| about: | ||
| home: https://github.com/refresh-bio/vclust | ||
| summary: "Fast and accurate tool for calculating ANI and clustering virus genomes and metagenomes." | ||
| license: GPL-3.0-or-later | ||
| license_family: GPL3 | ||
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| test: | ||
| #source_files: | ||
| # - example/*.* | ||
| # - example/output/*.* | ||
| #requires: | ||
| # - pytest | ||
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There was a problem hiding this comment. Please remove the commented out lines |
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| commands: | ||
| - vclust.py --help | ||
| - vclust.py info | ||
| #- vclust.py prefilter -i example/multifasta.fna -o tmp/filter.txt --batch-size 4 --k 18 | ||
| #- cmp tmp/filter.txt example/output/fltr.txt | ||
| #- vclust.py align -i example/multifasta.fna -o tmp/ani.tsv | ||
| #- cmp tmp/ani.tsv example/output/ani.tsv | ||
| #- vclust.py cluster -i tmp/ani.tsv -o tmp/clusters.tsv --ids tmp/ani.ids.tsv --tani 0.95 | ||
| #- cmp tmp/clusters.tsv example/output/clusters.tsv | ||
| #- pytest test.py # [linux] | ||
| #- pytest test.py -k 'not test_cluster_algorithm_leiden' # [osx] | ||
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There was a problem hiding this comment. 🛠️ Refactor suggestion Review and update the test section. The test section includes a mix of active and commented-out commands. While the active commands check basic functionality, which aligns with the PR objective of distributing precompiled libraries temporarily, consider the following:
Example of potential updates: test:
commands:
- vclust.py --help
- vclust.py info
- vclust.py prefilter -i example/multifasta.fna -o tmp/filter.txt --batch-size 4 --k 18
- cmp tmp/filter.txt example/output/fltr.txt
# Add more relevant tests herePlease review and update the test section accordingly to ensure comprehensive testing of the precompiled libraries. |
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| extra: | ||
| additional-platforms: | ||
| - linux-aarch64 | ||
| - osx-arm64 | ||
| skip-lints: | ||
| - should_be_noarch_generic | ||
| - should_not_be_noarch_source | ||
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🛠️ Refactor suggestion
Consider adding pytest to host requirements.
The Python requirement is correctly specified for both host and run environments. However, as pytest is used in the test section (although currently commented out), it should be added to the host requirements to ensure it's available during package building and testing.
Add pytest to the host requirements:
This change will help prevent potential issues during package testing.