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Update vcf-validator to v0.10.0 #51421

Merged
merged 8 commits into from
Oct 16, 2024
Merged

Update vcf-validator to v0.10.0 #51421

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e457803
Retrieve the prebuilt binaries
tcezard Mar 1, 2024
1cc295e
Build from source 1
tcezard Mar 1, 2024
bf19635
add default_ext_library_flag
tcezard Mar 4, 2024
e682092
testing with new branch
tcezard Aug 12, 2024
efb6e00
remove build parameters
tcezard Sep 12, 2024
f1a7c84
Attempt with dynamic libraries on mac osx
tcezard Sep 27, 2024
fc9abc1
Add support for arm64 on OS-X
tcezard Sep 30, 2024
ce4d23b
Update to the latest tag
tcezard Oct 1, 2024
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71 changes: 0 additions & 71 deletions recipes/vcf-validator/LICENSE_ODB
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This file was deleted.

19 changes: 15 additions & 4 deletions recipes/vcf-validator/build.sh
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Original file line number Diff line number Diff line change
@@ -1,6 +1,17 @@
mkdir -p ${PREFIX}/bin
#!/bin/bash

mv vcf_validator* ${PREFIX}/bin/vcf_validator
mv vcf_assembly_checker* ${PREFIX}/bin/vcf_assembly_checker
# Set c++ to version 11
export CXXFLAGS="-std=c++11 ${CXXFLAGS}"

chmod 755 ${PREFIX}/bin/vcf_assembly_checker ${PREFIX}/bin/vcf_validator
mkdir build || { echo "Failed to create build directory" >&2; exit 1; }
cd build || { echo "Failed to go into build directory" >&2; exit 1; }
cmake -G "Unix Makefiles" ..
make -j2 || { echo "Build failed" >&2; exit 1; }
cd .. || { echo "Failed to return to parent directory" >&2; exit 1; }
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🛠️ Refactor suggestion

Use dynamic CPU count for parallel compilation

Instead of hardcoding -j2, use ${CPU_COUNT} to utilize the available CPU cores. This makes the build process more efficient on systems with different numbers of cores.

Apply this change:

-make -j2 || { echo "Build failed" >&2; exit 1; }
+make -j${CPU_COUNT} || { echo "Build failed" >&2; exit 1; }
📝 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.

Suggested change
make -j2 || { echo "Build failed" >&2; exit 1; }
make -j${CPU_COUNT} || { echo "Build failed" >&2; exit 1; }

if ! ./build/bin/test_validation_suite; then
echo "Validation suite failed" >&2
exit 1
fi
cp build/bin/vcf_validator ${PREFIX}/bin
Comment on lines +11 to +14
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⚠️ Potential issue

Check for the existence of the validation suite before execution

Before running ./build/bin/test_validation_suite, ensure that the file exists to avoid execution errors.

Apply this change:

+if [ ! -f ./build/bin/test_validation_suite ]; then
+  echo "Validation suite executable not found" >&2
+  exit 1
+fi
 if ! ./build/bin/test_validation_suite; then
   echo "Validation suite failed" >&2
   exit 1
 fi
📝 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.

Suggested change
if ! ./build/bin/test_validation_suite; then
echo "Validation suite failed" >&2
exit 1
fi
if [ ! -f ./build/bin/test_validation_suite ]; then
echo "Validation suite executable not found" >&2
exit 1
fi
if ! ./build/bin/test_validation_suite; then
echo "Validation suite failed" >&2
exit 1
fi

cp build/bin/vcf_assembly_checker ${PREFIX}/bin
echo "Done with vcf-validator"
Comment on lines +15 to +16
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⚠️ Potential issue

Add error handling for copying binaries

Currently, the cp commands lack error handling. If the copy operation fails, the script will proceed without indication of an error.

Apply this change:

-cp build/bin/vcf_validator ${PREFIX}/bin
-cp build/bin/vcf_assembly_checker ${PREFIX}/bin
+cp build/bin/vcf_validator ${PREFIX}/bin || { echo "Failed to copy vcf_validator" >&2; exit 1; }
+cp build/bin/vcf_assembly_checker ${PREFIX}/bin || { echo "Failed to copy vcf_assembly_checker" >&2; exit 1; }
📝 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.

Suggested change
cp build/bin/vcf_validator ${PREFIX}/bin
cp build/bin/vcf_assembly_checker ${PREFIX}/bin
cp build/bin/vcf_validator ${PREFIX}/bin || { echo "Failed to copy vcf_validator" >&2; exit 1; }
cp build/bin/vcf_assembly_checker ${PREFIX}/bin || { echo "Failed to copy vcf_assembly_checker" >&2; exit 1; }

50 changes: 31 additions & 19 deletions recipes/vcf-validator/meta.yaml
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Original file line number Diff line number Diff line change
@@ -1,25 +1,40 @@
{% set name = "vcf-validator" %}
{% set version = "0.9.7" %}
{% set version = "0.10.0" %}

package:
name: {{ name }}
name: {{ name|lower }}
version: {{ version }}

source:
- url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_validator_linux # [linux]
sha256: 49aef4841cd7d0913ba12020465830b834ccfe20f2094222c8c41511f6c801ac # [linux]
- url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_assembly_checker_linux # [linux]
sha256: a9a00303c05c1fb5a33a5bd1f5c74fb5d8097f92a1f3ee815e19c137c0e26f13 # [linux]
- url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_validator_macos_x64 # [osx and x86]
sha256: 0b97a34fac6cf23951ffc33cdfb7b0602a89b4d5390564c8d816cb83019a3ffc # [osx and x86]
- url: https://github.com/EBIvariation/vcf-validator/releases/download/v{{ version }}/vcf_assembly_checker_macos_x64 # [osx and x86]
sha256: 1b5404a4239da9f5e5e39bece975e4eea55d87c486121a076226829b79477bc3 # [osx and x86]
url: https://github.com/EBIvariation/vcf-validator/archive/refs/tags/v{{ version }}.tar.gz
sha256: b46117700445644e6fc5a6d2655b477902c67aba0e7abe8a62df6cb49f923fff

build:
script:
number: 0
run_exports:
- {{ pin_subpackage(name, max_pin="x.x") }}
- {{ pin_subpackage("vcf-validator", max_pin="x.x") }}

requirements:
host:
- libboost-devel
- libcurl
build:
- {{ compiler('c') }}
- {{ compiler('cxx') }}
- make
- cmake >=2.8
- libboost-devel
- libtool
- zstd
- c-ares
- libcurl
- openssl
- bzip2
- libzlib
run:
- zstd
- libcurl

test:
commands:
Expand All @@ -28,17 +43,14 @@ test:

about:
home: https://github.com/EBIVariation/vcf-validator
summary: EBI EVA - Validation tool to ensure VCF specification compliance
summary: EBI EVA - Validation tool for VCF file format compliance
license: Apache-2.0
license_file:
- LICENSE
- LICENSE_ODB
license_file: LICENSE

extra:
additional-platforms:
- osx-arm64
recipe-maintainers:
- apriltuesday
- tcezard
- ebi-variation
skip-lints:
- should_be_noarch_generic
- should_not_be_noarch_source
- ebi-variation
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