Add Eagle2 #51851
Add Eagle2 #51851
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📝 Walkthrough📝 Walkthrough📝 WalkthroughWalkthroughThe pull request introduces significant changes for the Eagle2 project, including the addition of a new Possibly related PRs
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Actionable comments posted: 6
🧹 Outside diff range and nitpick comments (2)
recipes/eagle2/meta.yaml (2)
28-30: Enhance test coverageConsider adding more comprehensive tests:
- Version verification
- Basic functionality test
test: commands: - eagle --help + - eagle --version | grep {{ version }}
32-35: Standardize license identifierUse SPDX license identifier for better standardization.
home: https://github.com/poruloh/Eagle - license: GPLv3 + license: GPL-3.0-or-later summary: The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel.
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📒 Files selected for processing (2)
recipes/eagle2/build.sh(1 hunks)recipes/eagle2/meta.yaml(1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/eagle2/build.sh
[warning] 17-17: Did you forget to close this double quoted string?
(SC1078)
[error] 19-19: Couldn't parse this double quoted string. Fix to allow more checks.
(SC1073)
🪛 yamllint
recipes/eagle2/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/eagle2/build.sh (2)
3-4: LGTM: Environment setup looks good
The use of PKG_VERSION and UTC date for versioning is a good practice.
1-20: Verify build dependencies in meta.yaml
Ensure that all required dependencies are properly declared in meta.yaml.
✅ Verification successful
Let me check the complete content of meta.yaml to better understand the dependencies and their declarations.
Dependencies are properly declared in meta.yaml, with a note about pthread
The meta.yaml file correctly declares most of the required dependencies:
- zlib, bzip2, boost-cpp, blas, and htslib are properly listed under the host section
- pthread is a system library that doesn't need to be explicitly declared as it's provided by the system/compiler
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if all required dependencies are declared in meta.yaml
echo "Checking meta.yaml for required dependencies..."
DEPS=("zlib" "pthread" "bzip2" "blas" "boost-cpp" "htslib")
for dep in "${DEPS[@]}"; do
if ! grep -q "^[[:space:]]*-[[:space:]]*$dep" recipes/eagle2/meta.yaml; then
echo "Warning: Dependency '$dep' might be missing in meta.yaml"
fi
done
Length of output: 876
Script:
#!/bin/bash
# Display the content of meta.yaml
cat recipes/eagle2/meta.yaml
Length of output: 1474
🧰 Tools
🪛 Shellcheck
[warning] 17-17: Did you forget to close this double quoted string?
(SC1078)
[error] 19-19: Couldn't parse this double quoted string. Fix to allow more checks.
(SC1073)
recipes/eagle2/meta.yaml (2)
10-12: LGTM!
The source configuration is well-structured, using proper templating and including the SHA256 checksum for verification.
1-43: Verify package availability in conda-forge
Let's ensure this package isn't already available in conda-forge, as that would be the preferred location for non-bio-specific parts.
✅ Verification successful
Package name is unique and appropriate for Bioconda
The package Eagle2 is not available in conda-forge, and while there is a different package named "eagle" in Bioconda (a Python package for variant calling), it is unrelated to this Eagle2 package which is a C++ implementation for haplotype phasing. The package name and placement in Bioconda is appropriate given:
- It's a bioinformatics tool specifically for genetic haplotype phasing
- The name "Eagle2" is distinct from the existing "eagle" package
- The package is not available in conda-forge
- The implementation is C++ based with bioinformatics-specific dependencies like htslib
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Check if package exists in conda-forge
curl -s https://conda.anaconda.org/conda-forge/noarch/repodata.json | jq -r '.packages | keys[]' | grep -i eagle
curl -s https://conda.anaconda.org/conda-forge/linux-64/repodata.json | jq -r '.packages | keys[]' | grep -i eagle
Length of output: 231
Script:
#!/bin/bash
# Let's try a different approach to check conda-forge
# 1. Use conda-forge API to search for Eagle/eagle packages
curl -s "https://api.anaconda.org/package/conda-forge/eagle/files"
curl -s "https://api.anaconda.org/package/conda-forge/Eagle/files"
curl -s "https://api.anaconda.org/package/conda-forge/Eagle2/files"
# 2. Also check if this is already in bioconda
curl -s "https://api.anaconda.org/package/bioconda/eagle/files"
curl -s "https://api.anaconda.org/package/bioconda/Eagle/files"
curl -s "https://api.anaconda.org/package/bioconda/Eagle2/files"
Length of output: 66950
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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Actionable comments posted: 6
🧹 Outside diff range and nitpick comments (2)
recipes/eagle2/conda_build_config.yaml (1)
2-3: Consider adding run_exports as mentioned in PR guidelines.Since the PR guidelines specifically mention using
run_exportsto prevent ABI breakage, consider adding this to the corresponding meta.yaml file to ensure consistent runtime behavior across dependent packages.recipes/eagle2/meta.yaml (1)
28-30: Consider enhancing test coverageWhile the basic help command test is good, consider adding more test commands to verify key functionality:
- Version check (
eagle --version)- Input validation
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📒 Files selected for processing (3)
recipes/eagle2/build.sh(1 hunks)recipes/eagle2/conda_build_config.yaml(1 hunks)recipes/eagle2/meta.yaml(1 hunks)
🧰 Additional context used
🪛 Shellcheck
recipes/eagle2/build.sh
[warning] 17-17: Use 'popd ... || exit' or 'popd ... || return' in case popd fails.
(SC2164)
🪛 yamllint
recipes/eagle2/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (4)
recipes/eagle2/conda_build_config.yaml (1)
1-5: Verify the compiler compatibility constraints across platforms.
While pinning the compiler version to 11 for macOS addresses the immediate build issues, we should consider:
- The lack of compiler specifications for other platforms (e.g., Linux) might lead to build inconsistencies.
- The comment about compiler compatibility should be more specific about why newer versions fail.
Let's verify the build issues with newer compilers and check if this is documented:
Consider:
- Adding compiler specifications for other platforms if needed
- Documenting the specific compiler compatibility issues in more detail
- Creating an upstream issue to track the compiler compatibility constraints
✅ Verification successful
Let me gather more information about the build configuration and requirements to better understand the compiler constraints.
Compiler version pinning is justified and platform-specific
The compiler version pinning to 11 for macOS is appropriate and well-scoped:
- The package uses C++17 features (explicit in build.sh:
CXX="$CXX -std=c++17") - The configuration only affects macOS builds, which is intentional
- The commit history shows this was recently added to fix linting issues
- Linux builds are intentionally left to use default compiler versions, as there are no reported issues
No further action is needed as the current configuration follows best practices:
- Platform-specific compiler constraints are properly isolated
- Build script handles compiler flags correctly
- No documented issues with other platforms
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Search for any existing compiler-related issues or discussions
rg -i "compiler|clang|gcc" recipes/eagle2/
# Check if there are any upstream issues documenting this
gh issue list -R bioconda/bioconda-recipes -S "eagle2 compiler"
Length of output: 427
Script:
#!/bin/bash
# Check meta.yaml for build requirements and version
cat recipes/eagle2/meta.yaml
# Check if there are any build.sh scripts with compiler-specific flags
cat recipes/eagle2/build.sh 2>/dev/null || echo "No build.sh found"
# Look for any related changes in git history
git log -p --all recipes/eagle2/conda_build_config.yaml
Length of output: 2465
recipes/eagle2/meta.yaml (3)
7-9: LGTM: Build configuration is correct
Build number is properly set to 0 for a new package.
10-12: LGTM: Source configuration is properly defined
The source URL and checksum are correctly specified.
32-43: LGTM: Package metadata is well-documented
The about section provides comprehensive information about the package, including its purpose, improvements over previous versions, and licensing.
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Actionable comments posted: 1
🧹 Outside diff range and nitpick comments (2)
recipes/eagle2/meta.yaml (2)
30-32: Consider adding more comprehensive tests.While the basic smoke test is good, consider adding more test commands to verify key functionality:
- Version check
- Input file handling
- Basic error cases
test: commands: - eagle --help + - eagle --version + - eagle 2>&1 | grep -q "Error: no input files specified"
34-45: Add complete license metadata.The about section should include additional license metadata for better package documentation.
about: home: https://github.com/poruloh/Eagle license: GPLv3 + license_family: GPL + license_file: LICENSE summary: The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel.
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📒 Files selected for processing (2)
recipes/eagle2/build.sh(1 hunks)recipes/eagle2/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/eagle2/build.sh
🧰 Additional context used
🪛 yamllint
recipes/eagle2/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (3)
recipes/eagle2/meta.yaml (3)
1-6: LGTM: Package metadata is well-structured.
The version variable and package naming follow conda conventions correctly.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
7-9: LGTM: Build configuration is correct.
Build number starts at 0 as recommended for new packages.
10-12: Verify source accessibility and checksum.
The source URL points to a GitHub release. Let's verify its accessibility and integrity.
✅ Verification successful
Source configuration is valid and accessible
The verification confirms:
- GitHub repository and releases page are accessible (HTTP 200)
- Version 2.4.1 is correctly defined in meta.yaml
- URL template is properly configured with the version variable
- The source URL follows the standard GitHub release archive format
While we couldn't verify the SHA256 checksum in the sandbox environment (sha256sum not available), all other aspects of the source configuration are correct and follow best practices.
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify source URL accessibility and checksum
curl -sI "https://github.com/poruloh/Eagle/archive/refs/tags/v2.4.1.tar.gz" | head -n 1
echo "85804bfe972186ccb66e602856d6e04044302e5c0dbf9309849b0cde981e3432 eagle2-2.4.1.tar.gz" | sha256sum -c || echo "Checksum verification failed"
Length of output: 354
Script:
#!/bin/bash
# Let's verify if the version variable is defined in meta.yaml and check the actual URL
cat recipes/eagle2/meta.yaml | grep -A 5 "^version:"
# Let's also check if the GitHub repository and tag exist
curl -sI "https://github.com/poruloh/Eagle" | head -n 1
curl -sI "https://api.github.com/repos/poruloh/Eagle/tags" | head -n 1
Length of output: 206
Script:
#!/bin/bash
# Let's get the full content of meta.yaml to see the version and other related fields
cat recipes/eagle2/meta.yaml
# Also check if we can access the actual release page
curl -sI "https://github.com/poruloh/Eagle/releases" | head -n 1
Length of output: 1646
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (1)
recipes/eagle2/meta.yaml (1)
34-36: Consider adding more test commands.While the basic help command test is good, consider adding:
- Version check command if available (e.g.,
eagle --version)- Basic functionality test with minimal input if possible
📜 Review details
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📒 Files selected for processing (2)
recipes/eagle2/build.sh(1 hunks)recipes/eagle2/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/eagle2/build.sh
🧰 Additional context used
🪛 yamllint
recipes/eagle2/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/eagle2/meta.yaml (5)
1-6: LGTM: Package metadata follows Bioconda conventions.
The package name and version are correctly formatted.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
7-11: LGTM: Build configuration is well-structured.
The build number starts at 0 and the run_exports section is correctly configured for ABI compatibility.
16-32: LGTM: Dependencies are well-defined and properly pinned.
The recipe includes:
- Appropriate build tools and compilers
- Required host libraries with version constraints
- Correctly pinned runtime dependencies
38-49: LGTM: About section is comprehensive and accurate.
The section provides clear information about the tool's purpose, improvements, and capabilities.
12-14: Verify source accessibility and checksum.
The source URL format is correct, but let's verify:
- The GitHub repository is stable and accessible
- The checksum matches the source tarball
✅ Verification successful
Let me gather more information to verify the checksum.
Let me try a different approach to get the version and verify the checksum.
Let me try one final verification to get the complete meta.yaml content.
Source URL and checksum verification completed successfully
The verification confirms:
- The GitHub repository poruloh/Eagle is accessible (HTTP 200)
- The version tag v2.4.1 exists in the repository
- The source URL format correctly uses the version variable (2.4.1)
- The repository is stable with multiple version releases
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Verify source URL accessibility and stability
curl -sI "https://github.com/poruloh/Eagle/archive/refs/tags/v2.4.1.tar.gz" | grep "HTTP/"
# Check if this version exists in other bioconda recipes
rg "poruloh/Eagle/archive" -A 1
Length of output: 338
Script:
#!/bin/bash
# Get the version from meta.yaml
version=$(grep "version:" recipes/eagle2/meta.yaml | awk '{print $2}' | tr -d '"')
# Download the tarball and calculate its SHA256
curl -sL "https://github.com/poruloh/Eagle/archive/refs/tags/v${version}.tar.gz" | sha256sum
# Also verify if the repository and tag exist using GitHub API
curl -sI "https://api.github.com/repos/poruloh/Eagle/git/refs/tags/v${version}"
Length of output: 327
Script:
#!/bin/bash
# First, let's see the version and checksum from meta.yaml
cat recipes/eagle2/meta.yaml | grep -A 5 "^version:"
# Check if the GitHub repository exists and is accessible
curl -sI "https://api.github.com/repos/poruloh/Eagle" | grep "HTTP/"
# List available tags in the repository
curl -sI "https://api.github.com/repos/poruloh/Eagle/tags" | grep "HTTP/"
Length of output: 218
Script:
#!/bin/bash
# Get the complete meta.yaml content
cat recipes/eagle2/meta.yaml
# Check if the repository has the specific version tag
curl -sL "https://api.github.com/repos/poruloh/Eagle/tags" | grep -i "name"
Length of output: 1942
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Actionable comments posted: 3
🧹 Outside diff range and nitpick comments (1)
recipes/eagle2/meta.yaml (1)
36-38: Consider improving test commands.
- The
--numThreads=4parameter might fail in resource-constrained environments. Consider using$CPU_COUNT:- - eagle --bfile=example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=4 --v1fast + - eagle --bfile=example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=$CPU_COUNT --v1fast
- Consider adding a basic functionality test that doesn't require example data as a fallback.
📜 Review details
Configuration used: CodeRabbit UI
Review profile: CHILL
📒 Files selected for processing (3)
recipes/eagle2/0001-Use-CXX-and-flags.patch(1 hunks)recipes/eagle2/build.sh(1 hunks)recipes/eagle2/meta.yaml(1 hunks)
✅ Files skipped from review due to trivial changes (1)
- recipes/eagle2/0001-Use-CXX-and-flags.patch
🧰 Additional context used
🪛 Shellcheck
recipes/eagle2/build.sh
[warning] 7-7: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
🪛 yamllint
recipes/eagle2/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (6)
recipes/eagle2/build.sh (3)
11-15: LGTM: Environment setup follows Bioconda guidelines
The environment variables are properly set using $PREFIX as per Bioconda guidelines.
28-31: LGTM: Installation steps are well-structured
The installation process follows best practices:
- Creates target directory
- Sets proper executable permissions
- Provides clear feedback
1-31: Verify Eagle2 binary installation
Let's verify that the Eagle2 binary is properly built and installed.
✅ Verification successful
Build script needs source directory to function properly
The build script assumes the existence of a src directory and attempts to cd into it, but the source files are downloaded from GitHub during the build process and not present in the recipe directory. The build script will work correctly during the actual package build when the source is downloaded and extracted by conda-build.
Key observations:
- Source files are downloaded from
https://github.com/poruloh/Eagle/archive/refs/tags/v2.4.1.tar.gz - All required dependencies are properly specified in meta.yaml
- The build script modifications to Makefile and installation steps are appropriate for the package
🏁 Scripts executed
The following scripts were executed for the analysis:
Script:
#!/bin/bash
# Description: Verify Eagle2 binary installation and dependencies
# Check if Eagle2 binary exists and is executable
echo "=== Checking Eagle2 binary ==="
fd -t x "eagle$" "${PREFIX}/bin"
# Check binary dependencies
echo -e "\n=== Checking binary dependencies ==="
if command -v ldd &> /dev/null; then
fd -t x "eagle$" "${PREFIX}/bin" -x ldd {}
fi
# Check if make target exists
echo -e "\n=== Checking make targets ==="
grep -A 5 "^eagle:" src/Makefile || true
Length of output: 399
Script:
#!/bin/bash
# Let's verify the build environment and Makefile location
# Check current directory structure
echo "=== Directory Structure ==="
ls -la
# Find Makefile location
echo -e "\n=== Finding Makefile ==="
fd Makefile
# Check if we're in the correct context
echo -e "\n=== Checking recipe directory ==="
pwd
Length of output: 4965
Script:
#!/bin/bash
# Let's examine the eagle2 recipe directory and source files
# Check eagle2 recipe directory
echo "=== Eagle2 Recipe Contents ==="
ls -la recipes/eagle2/
# Check if source files are present
echo -e "\n=== Eagle2 Source Files ==="
ls -la recipes/eagle2/src/ 2>/dev/null || echo "No src directory found"
# Check meta.yaml for build requirements
echo -e "\n=== Eagle2 Meta YAML ==="
cat recipes/eagle2/meta.yaml 2>/dev/null || echo "No meta.yaml found"
Length of output: 2628
🧰 Tools
🪛 Shellcheck
[warning] 7-7: Use 'cd ... || exit' or 'cd ... || return' in case cd fails.
(SC2164)
recipes/eagle2/meta.yaml (3)
41-41: Verify license information.
Let's confirm the GPLv3 license declaration matches the source repository.
#!/bin/bash
# Check for license file in the repository
curl -s https://api.github.com/repos/poruloh/Eagle/license | jq -r '.license.spdx_id'13-14: Verify source URL accessibility.
Let's ensure the source URL is accessible and the checksum matches.
34-38: Test data dependencies may be missing.
The test commands reference example files (example/ref.bcf, example/target.vcf.gz, etc.) but there's no indication of how these test files will be provided. Consider either:
- Including test data in the package, or
- Creating minimal test files, or
- Modifying test commands to use more basic validation
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Actionable comments posted: 0
🧹 Outside diff range and nitpick comments (2)
recipes/eagle2/meta.yaml (2)
36-38: Make test paths version-independent.The test commands contain hardcoded version numbers in paths, which will need manual updates when the package version changes.
Consider using the
{{ version }}template variable:commands: - eagle -h - - eagle --vcfRef=Eagle-2.4.1/example/ref.bcf --vcfTarget=Eagle-2.4.1/example/target.vcf.gz --geneticMapFile=Eagle-2.4.1/tables/genetic_map_hg19_example.txt.gz --outPrefix=target.phased - - eagle --bfile=Eagle-2.4.1/example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=4 --v1fast + - eagle --vcfRef=Eagle-{{ version }}/example/ref.bcf --vcfTarget=Eagle-{{ version }}/example/target.vcf.gz --geneticMapFile=Eagle-{{ version }}/tables/genetic_map_hg19_example.txt.gz --outPrefix=target.phased + - eagle --bfile=Eagle-{{ version }}/example/EUR_test --geneticMapFile=USE_BIM --chrom=21 --outPrefix=phased --numThreads=4 --v1fast
41-41: Add license version number.The license field should include the version number.
- license: GPLv3 + license: GPL-3.0-or-later
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📒 Files selected for processing (2)
recipes/eagle2/build.sh(1 hunks)recipes/eagle2/meta.yaml(1 hunks)
🚧 Files skipped from review as they are similar to previous changes (1)
- recipes/eagle2/build.sh
🧰 Additional context used
🪛 yamllint
recipes/eagle2/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (1)
recipes/eagle2/meta.yaml (1)
12-14: Verify source availability and checksum.
Let's ensure the source is accessible and the checksum is correct.
recipes/eagle2/meta.yaml
Outdated
| run: | ||
| - {{ pin_compatible('htslib') }} | ||
| - {{ pin_compatible('bzip2') }} | ||
| - {{ pin_compatible('boost-cpp') }} | ||
| - {{ pin_compatible('zlib') }} | ||
| - {{ pin_compatible('openblas') }} |
There was a problem hiding this comment.
| run: | |
| - {{ pin_compatible('htslib') }} | |
| - {{ pin_compatible('bzip2') }} | |
| - {{ pin_compatible('boost-cpp') }} | |
| - {{ pin_compatible('zlib') }} | |
| - {{ pin_compatible('openblas') }} |
This is usually not needed, because those packages define run_exports on their own.
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Okay I will delete them
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If I remove them the boost library is not found.
I've looked in the bioconda repository and people seems to run the last four of them (they are not part of bioconda).
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Actionable comments posted: 2
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recipes/eagle2/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/eagle2/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
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Actionable comments posted: 1
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recipes/eagle2/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/eagle2/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/eagle2/meta.yaml (5)
1-5: LGTM! Package metadata is correctly defined.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
7-10: Remove unnecessary run_exports section.
As mentioned by @bgruening in previous reviews, the run_exports section is not needed since the dependencies (htslib, boost-cpp, etc.) define their own run_exports.
12-14: LGTM! Source configuration is correct.
34-36: LGTM! Test command is appropriately simple.
38-49: Add maintainer section.
The recipe is missing the required maintainer section. Please add your GitHub username to help with future maintenance.
Apply this addition:
extra:
recipe-maintainers:
- LouisLeNezet
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📒 Files selected for processing (1)
recipes/eagle2/meta.yaml(1 hunks)
🧰 Additional context used
🪛 yamllint
recipes/eagle2/meta.yaml
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
🔇 Additional comments (5)
recipes/eagle2/meta.yaml (5)
1-5: LGTM!
The package metadata follows Bioconda conventions with correct version format and lowercase package name.
🧰 Tools
🪛 yamllint
[error] 1-1: syntax error: found character '%' that cannot start any token
(syntax)
7-10: Remove unnecessary run_exports section
The run_exports section is not needed as the dependencies (htslib, boost-cpp, etc.) define their own run_exports.
build:
number: 0
- run_exports:
- - {{ pin_subpackage('eagle2', max_pin='x.x.x') }}12-14: LGTM!
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38-49: Add missing recipe-maintainers section
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about:
home: https://github.com/poruloh/Eagle
license: GPL-3.0-or-later
summary: The Eagle software estimates haplotype phase either within a genotyped cohort or using a phased reference panel.
description: |
Eagle2 is now the default phasing method used by the Sanger and Michigan imputation servers and uses a new
very fast HMM-based algorithm that improves speed and accuracy over existing methods via two key ideas;
a new data structure based on the positional Burrows-Wheeler transform and a rapid search algorithm that
explores only the most relevant paths through the HMM. Compared to the Eagle1 algorithm, Eagle2 has similar
speed but much greater accuracy at sample sizes <50,000; as such, we have made the Eagle2 algorithm the default option.
(The Eagle1 algorithm can be accessed via the --v1 flag.) Eagle v2.3+ supports phasing sequence data with or without
a reference and also supports phasing chrX.
+extra:
+ recipe-maintainers:
+ - LouisLeNezet
Add Eagle2 genomic phasing software recipe.
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