Add ntsm recipe https://github.com/JustinChu/ntsm #52262
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📝 WalkthroughWalkthroughThis pull request introduces several new files and configurations for the Possibly related PRs
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (1)
recipes/ntsm/meta.yaml (1)
32-37: Enhance test coverage.Current tests only verify command availability. Consider adding:
- Version checks for each command
- Basic functionality tests with minimal example data
commands: - ntsmCount --help - ntsmVCF --help - ntsmEval --help - ntsmSiteGen -h + - ntsmCount --version + - ntsmVCF --version + - ntsmEval --version + - ntsmSiteGen --version
📜 Review details
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📒 Files selected for processing (3)
recipes/ntsm/LICENSE(1 hunks)recipes/ntsm/build.sh(1 hunks)recipes/ntsm/meta.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (2)
- recipes/ntsm/LICENSE
- recipes/ntsm/build.sh
🧰 Additional context used
🪛 yamllint
recipes/ntsm/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/ntsm/meta.yaml (5)
1-5: LGTM! Package metadata follows conda conventions.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
39-46: LGTM! Package metadata is complete.
7-9: Verify source URL accessibility and checksum.
11-13: Verify OSX compatibility restriction.
The recipe skips OSX builds, but the requirements include OSX-specific dependencies (llvm-openmp). This seems inconsistent.
48-50: Verify ARM64 compatibility.
The recipe adds support for linux-aarch64, but we should verify that:
- The source code has no x86-specific assembly
- All dependencies are available for ARM64
✅ Verification successful
Let me analyze the search results and generate additional verification scripts to check for architecture-specific code.
The first search showed some x86 references but they were mostly in unrelated packages. Let's check the specific recipe and its dependencies to verify ARM64 compatibility.
Let me analyze the recipe and generate one final verification script to check the source code.
This will help verify if there are any architecture-specific implementations in the source code.
ARM64 support appears compatible
The package should work on ARM64 architecture because:
- No architecture-specific assembly code or intrinsics were found
- The dependencies (zlib, libgomp, samtools, bwa, perl) are all available for ARM64
- The code appears to be pure C++ without any architecture-specific optimizations
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Check for architecture-specific code
# Search for assembly or architecture-specific code
rg -i "asm|__asm__|__attribute__|SIMD|SSE|AVX|x86"
Length of output: 158186
Script:
#!/bin/bash
# Search for assembly files and architecture-specific code in the recipe and source
rg -i "assembly|arch|x86|arm|aarch" recipes/ntsm/
# Check build scripts and dependencies
cat recipes/ntsm/meta.yaml
Length of output: 1111
Script:
#!/bin/bash
# Check source code for any architecture-specific code or assembly
cd recipes/ntsm/
# Look for architecture-specific code patterns in source files
rg -i "asm|simd|avx|sse|intrinsic|x86|amd64|arm|aarch" .
# Check if there are any assembly files
find . -type f -name "*.s" -o -name "*.asm" -o -name "*.S"
Length of output: 170
recipes/ntsm/meta.yaml
Outdated
| requirements: | ||
| build: | ||
| - {{ compiler('cxx') }} | ||
| - llvm-openmp # [osx] | ||
| - make | ||
| host: | ||
| - zlib | ||
| - libgomp | ||
| run: | ||
| - llvm-openmp # [osx] | ||
| - zlib | ||
| - libgomp | ||
| - make | ||
| - samtools | ||
| - bwa | ||
| - perl |
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🛠️ Refactor suggestion
Add version constraints for runtime dependencies.
Consider adding version constraints for critical dependencies like samtools, bwa, and perl to ensure reproducibility and prevent potential compatibility issues.
Additionally, there might be a conflict between libgomp and llvm-openmp if OSX builds are enabled in the future.
run:
- llvm-openmp # [osx]
- zlib
- libgomp
- make
- - samtools
- - bwa
- - perl
+ - samtools >=1.15
+ - bwa >=0.7.17
+ - perl >=5.26📝 Committable suggestion
‼️ IMPORTANT
Carefully review the code before committing. Ensure that it accurately replaces the highlighted code, contains no missing lines, and has no issues with indentation. Thoroughly test & benchmark the code to ensure it meets the requirements.
| requirements: | |
| build: | |
| - {{ compiler('cxx') }} | |
| - llvm-openmp # [osx] | |
| - make | |
| host: | |
| - zlib | |
| - libgomp | |
| run: | |
| - llvm-openmp # [osx] | |
| - zlib | |
| - libgomp | |
| - make | |
| - samtools | |
| - bwa | |
| - perl | |
| requirements: | |
| build: | |
| - {{ compiler('cxx') }} | |
| - llvm-openmp # [osx] | |
| - make | |
| host: | |
| - zlib | |
| - libgomp | |
| run: | |
| - llvm-openmp # [osx] | |
| - zlib | |
| - libgomp | |
| - make | |
| - samtools >=1.15 | |
| - bwa >=0.7.17 | |
| - perl >=5.26 |
recipes/ntsm/meta.yaml
Outdated
| - llvm-openmp # [osx] | ||
| - zlib | ||
| - libgomp | ||
| - make |
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Do you need 'make' to run the app ?
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Not for most parts of the program but for a pipeline generating a sites file from a vcf & genome fasta: https://github.com/JustinChu/ntsm/blob/main/ntsmSiteGen
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@BiocondaBot please add label |
Adding this nucleotide sequence sample swap detection tool: https://github.com/JustinChu/ntsm to bioconda.
Please read the guidelines for Bioconda recipes before opening a pull request (PR).
General instructions
@BiocondaBot please add labelcommand.@bioconda/corein a comment.Instructions for avoiding API, ABI, and CLI breakage issues
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