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Update svdss to 2.0.0 #51519

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merged 6 commits into from
Oct 21, 2024
Merged

Update svdss to 2.0.0 #51519

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32e79d5
Update svdss to 2.0.0
BiocondaBot Oct 21, 2024
74171b5
add run_exports
mencian Oct 21, 2024
b1cecfd
edit build.sh
mencian Oct 21, 2024
3dd7acb
edit build.sh
mencian Oct 21, 2024
9a9837a
edit build.sh
mencian Oct 21, 2024
63b9342
revert to skipping osx
mencian Oct 21, 2024
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30 changes: 22 additions & 8 deletions recipes/svdss/build.sh
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Original file line number Diff line number Diff line change
@@ -1,10 +1,24 @@
#!/usr/bin/env bash

mkdir -p build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DCONDAPREFIX=${PREFIX} ..
make
cd ..
#!/bin/bash

mkdir -p ${PREFIX}/bin
cp SVDSS ${PREFIX}/bin
export INCLUDE_PATH="${PREFIX}/include"
export LIBRARY_PATH="${PREFIX}/lib"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
export CFLAGS="${CFLAGS} -O3 -L${PREFIX}/lib"
export CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include"

if [[ `uname` == "Darwin" ]]; then
export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
else
export CONFIG_ARGS=""
fi

cmake -S. -B build -DCMAKE_BUILD_TYPE=Release \
-DCONDAPREFIX="${PREFIX}" -DCMAKE_CXX_COMPILER="${CXX}" \
-DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \
-DCMAKE_C_FLAGS="${CFLAGS}" \
"${CONFIG_ARGS}"
cmake --build build -j "${CPU_COUNT}" -v

chmod 0755 SVDSS
cp -f SVDSS ${PREFIX}/bin
104 changes: 0 additions & 104 deletions recipes/svdss/build_failure.linux-64.yaml
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This file was deleted.

27 changes: 19 additions & 8 deletions recipes/svdss/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{% set version = "1.0.5" %}
{% set sha256 = "98345630451e98a43af9c807c9cf739cce58f6582d860ceb5daa00bdb50950df" %}
{% set version = "2.0.0" %}
{% set sha256 = "825324dbdd70474b2a527925a25dea94b597ef579dee117645f285d678985652" %}

package:
name: svdss
Expand All @@ -10,8 +10,10 @@ source:
sha256: {{ sha256 }}

build:
number: 3
skip: True # [osx]
number: 0
#skip: True # [osx]
run_exports:
- {{ pin_subpackage('svdss', max_pin="x") }}
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💡 Codebase verification

macOS support may not be fully enabled.

  • The skip directive for macOS has been commented out.
  • macOS-specific dependencies like llvm-openmp are still present in meta.yaml (lines 30 and 38).
  • No macOS-specific build script (build-osx.sh) found.

Please review and ensure that all macOS support configurations are correctly implemented.

🔗 Analysis chain

Build section changes look good, but verify macOS support.

The build number has been correctly reset to 0 for the new version. The addition of the run_exports section is a good practice for ensuring correct version pinning.

The macOS skip directive has been commented out. Please confirm that the package now supports macOS by running the following script:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check for macOS-specific build instructions or dependencies

# Search for macOS-specific conditionals in the meta.yaml file
echo "macOS-specific conditionals in meta.yaml:"
grep -n '\[osx\]' recipes/svdss/meta.yaml

# Check if there's a separate macOS build script
if [ -f recipes/svdss/build-osx.sh ]; then
    echo "macOS-specific build script found: recipes/svdss/build-osx.sh"
else
    echo "No macOS-specific build script found."
fi

# Check for macOS-specific dependencies
echo "macOS-specific dependencies:"
grep -n '# \[osx\]' recipes/svdss/meta.yaml

Length of output: 864

Script:

#!/bin/bash
# Description: Verify macOS support by checking for conditionals and build scripts in meta.yaml

# Search for macOS-specific conditionals in meta.yaml
echo "Checking for macOS-specific conditionals in meta.yaml:"
grep -n '\[osx\]' recipes/svdss/meta.yaml || echo "No macOS-specific conditionals found."

# Check for the presence of a macOS-specific build script
echo "Checking for macOS-specific build script:"
if [ -f recipes/svdss/build-osx.sh ]; then
    echo "macOS-specific build script found: recipes/svdss/build-osx.sh"
else
    echo "No macOS-specific build script found."
fi

# Search for macOS-specific dependencies in meta.yaml
echo "Checking for macOS-specific dependencies in meta.yaml:"
grep -n '# \[osx\]' recipes/svdss/meta.yaml || echo "No macOS-specific dependencies found."

Length of output: 717


requirements:
build:
Expand All @@ -20,16 +22,20 @@ requirements:
- make
- automake
- autoconf
- coreutils
- cmake >=3.14
- libtool
- cmake
- git
host:
- libgomp # [linux]
- llvm-openmp # [osx]
- htslib
- gsl
- zlib
- bzip2
- xz
run:
- libgomp # [linux]
- llvm-openmp # [osx]
- samtools >=1.9
- bcftools >=1.9

Expand All @@ -38,12 +44,17 @@ test:
- SVDSS --version

about:
home: https://github.com/Parsoa/SVDSS
home: "https://github.com/Parsoa/SVDSS"
license: MIT
summary: Structural Variant Discovery from Sample-specific Strings
license_family: MIT
license_file: LICENSE
summary: "Structural Variant Discovery from Sample-specific Strings."
dev_url: "https://github.com/Parsoa/SVDSS"
doc_url: "https://github.com/Parsoa/SVDSS/blob/v{{ version }}/README.md"

extra:
identifiers:
- biotools:svdss
- doi:10.1038/s41592-022-01674-1
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💡 Codebase verification

DOI does not resolve correctly

The DOI 10.1038/s41592-022-01674-1 does not resolve. Please verify and correct the DOI in recipes/svdss/meta.yaml.

🔗 Analysis chain

DOI addition is excellent.

The inclusion of a DOI (Digital Object Identifier) is a valuable addition for academic citation and tracking of the software.

Please run the following script to verify the DOI:

The previous script did not verify the DOI as intended. Please run the following script to verify the DOI:

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Verify the DOI

# Extract the DOI
doi=$(grep -oP 'doi:\K[^\s]+' recipes/svdss/meta.yaml)

# Check if the DOI resolves
if curl -s -o /dev/null -w "%{http_code}" "https://doi.org/$doi" | grep -q "200"; then
    echo "DOI $doi is valid and resolves correctly."
else
    echo "Error: DOI $doi does not resolve. Please check the DOI."
fi

Length of output: 2219

Script:

#!/bin/bash
# Description: Verify the DOI

# Extract the DOI
doi=$(grep -oP 'doi:\K[^\s]+' recipes/svdss/meta.yaml)

# Check if the DOI resolves
if curl -s -o /dev/null -w "%{http_code}" "https://doi.org/$doi" | grep -q "200"; then
    echo "DOI $doi is valid and resolves correctly."
else
    echo "Error: DOI $doi does not resolve. Please check the DOI."
fi

Length of output: 346

recipe-maintainers:
- ldenti