Add amplici package in bioconda #51847
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Actionable comments posted: 5
🧹 Outside diff range and nitpick comments (2)
recipes/amplici/meta.yaml (2)
14-16: Remove or address the TODO comment.The comment about adding more critical dependencies should be removed if there are no additional dependencies to pin, or replaced with actual dependencies if needed.
run_exports: - {{ pin_subpackage("amplici", max_pin="x") }} - # Add more if there are other critical dependencies that require pinning
30-34: Minor improvements needed in the about section.Please:
- Remove trailing spaces after BSD in license_family
- Consider adding a license_file field to specify the location of the license file
about: home: https://github.com/DormanLab/AmpliCI license: BSD 3-Clause - license_family: BSD + license_family: BSD + license_file: LICENSE # Add the path to the license file🧰 Tools
🪛 yamllint
[error] 33-33: trailing spaces
(trailing-spaces)
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recipes/amplici/build.sh(1 hunks)recipes/amplici/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/amplici/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
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[error] 33-33: trailing spaces
(trailing-spaces)
🔇 Additional comments (3)
recipes/amplici/meta.yaml (3)
40-48: LGTM! Extra section is well-documented.
The section includes all necessary information:
- Additional platform support
- Recipe maintainer
- Appropriate identifiers (biotools and DOI)
1-48: Verify bioconda-specific requirements.
The package appears to be biologically relevant (handles amplicon sequences) which is appropriate for bioconda. However, please ensure:
- The package follows bioconda's naming conventions
- All dependencies are available in bioconda or conda-forge
#!/bin/bash
# Check if dependencies are available in bioconda/conda-forge
conda search -c bioconda -c conda-forge cmake make gfortran🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
[error] 33-33: trailing spaces
(trailing-spaces)
19-28: Consider adding run requirements and version constraints.
The recipe is missing:
- Run requirements section which typically specifies runtime dependencies
- Version constraints for cmake and other build dependencies
Please verify if the package has any runtime dependencies that should be listed.
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Actionable comments posted: 2
🧹 Outside diff range and nitpick comments (1)
recipes/amplici/build.sh (1)
3-7: Improve OS detection robustness.Good practice adding macOS-specific CMake configuration. Consider these improvements:
-if [[ `uname` == "Darwin" ]]; then +if [[ "$(uname)" == "Darwin" ]]; then
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recipes/amplici/build.sh(1 hunks)recipes/amplici/meta.yaml(1 hunks)
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recipes/amplici/build.sh
[warning] 9-9: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/amplici/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (8)
recipes/amplici/build.sh (1)
1-2: Add error handling at script start.
The script should include error handling flags to fail fast on errors.
recipes/amplici/meta.yaml (7)
1-6: LGTM! Version and package metadata are properly configured.
The version mismatch issue from the previous review has been resolved.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
11-15: LGTM! Build settings follow best practices.
The run_exports configuration will help maintain ABI compatibility.
26-32: LGTM! Package metadata is complete and well-documented.
All required fields are present, including license file reference and development URLs.
34-36: Previous suggestion for comprehensive tests still applies.
Referring to the previous review comment about adding more comprehensive tests.
38-46: LGTM! Extra metadata is comprehensive.
Excellent inclusion of platform support, maintainer information, and scientific identifiers.
16-25: Verify if run-time dependencies are needed.
While build and host dependencies look correct, there are no run-time dependencies specified. Please verify if the package requires any runtime dependencies, particularly:
- zlib (since it's a host dependency)
- Any runtime libraries needed for sequence processing
#!/bin/bash
# Description: Check for potential runtime dependencies
# Look for shared library dependencies in the source
rg -l "include.*zlib\.h|include.*stdlib\.h|include.*stdio\.h"7-10: Verify the source tarball checksum.
The URL format is correct, but let's verify the SHA256 checksum matches the source tarball.
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Edit the CMakeList file of AmpliCI
Update to use the latest version v2.2 of AmpliCI |
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Thanks @xiyupeng |
Add amplici package in bioconda.
This is the first contribut. Feel free to comment. Thanks!
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
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