From ce4d23b688e5fcb5f594f814d713568821067b19 Mon Sep 17 00:00:00 2001 From: tcezard Date: Tue, 1 Oct 2024 11:43:41 +0100 Subject: [PATCH] Update to the latest tag apply fixes for linting --- recipes/vcf-validator/LICENSE_ODB | 71 ------------------------------- recipes/vcf-validator/build.sh | 11 +++-- recipes/vcf-validator/meta.yaml | 32 ++++++-------- 3 files changed, 19 insertions(+), 95 deletions(-) delete mode 100644 recipes/vcf-validator/LICENSE_ODB diff --git a/recipes/vcf-validator/LICENSE_ODB b/recipes/vcf-validator/LICENSE_ODB deleted file mode 100644 index 52e36215fc329..0000000000000 --- a/recipes/vcf-validator/LICENSE_ODB +++ /dev/null @@ -1,71 +0,0 @@ - -ODB License Exception for vcf-validator (Validator for the Variant Call -Format (VCF)) Software - Version 1.0 - -1. Intent - -The intent of this License Exception is to allow the vcf-validator software -to use ODB without the "copyleft" restrictions that would normally be -imposed by the GPL, the license under which ODB is distributed. - -Specifically, the intent is to allow you to use the original vcf-validator -software in your open source or proprietary works without imposing -any additional restrictions to the terms and conditions of the -Apache 2.0 license used by vcf-validator. - -If you wish to modify the vcf-validator software in such a way that it -requires changes to the persistent object model handled by ODB, you can -continue enjoying the terms of this exception provided that you are -prepared to release your modifications under Apache 2.0 or another open -source license and you obtain a separate license exception for your -modifications from Code Synthesis Tools CC. - -While this exception is specific to vcf-validator, any open source software -project licensed under a more liberal than the GPL license can obtain -a similar exception free of charge by contacting Code Synthesis Tools CC. - -2. Definitions - -"Original Software" is the vcf-validator software, Copyright (c) EMBL - -European Bioinformatics Institute, distributed under the terms of the -Apache 2.0 license, and available to any third party from: - - https://github.com/ebivariation/vcf-validator - -"ODB-Extended Software" are any modifications to the Original Software -that require additions or changes to the persistent object model of -the Original Software that is handled by ODB. - -"Work Based on the Original Software" is any derivative work under the -copyright law that is either based on the Original Software or any -modified version of the Original Software that does not constitute -ODB-Extended Software. - -"Work Based on the ODB-Extended Software" is any derivative work under -the copyright law that is based on any modified version of the Original -Software that constitutes ODB-Extended Software. - -3. Legal Terms and Conditions - -As a special exception to the terms and conditions of version 2 of the -GPL you may use the ODB runtime libraries in Original Software and in -Works Based on the Original Software and distribute the resulting works -in object code or executable form and without making source code for -such works available to any third party, provided that all of the -following conditions are met: - - a) Original Software was licensed as a whole at no charge to all third - parties under the terms of the Apache 2.0 license. - - b) The ODB runtime libraries in Works Based on the Original Software - are used solely for the purpose of supporting the functionality of - the Original Software. - -The same exception does not apply automatically to ODB-Extended Software -or Works Based on the ODB-Extended Software. If you wish to enjoy this -exception for such works, then you will need to license ODB-Extended -Software at no charge to all third parties under the terms of the Apache 2.0 -license or another open source license. You will also need to obtain a -separate License Exception for ODB-Extended Software from Code Synthesis -Tools CC. diff --git a/recipes/vcf-validator/build.sh b/recipes/vcf-validator/build.sh index b480520206ed5..1b1bad0e5fa5a 100644 --- a/recipes/vcf-validator/build.sh +++ b/recipes/vcf-validator/build.sh @@ -1,11 +1,8 @@ #!/bin/bash -# Install additional dependencies -if [ -z ${OSX_ARCH+x} ]; then - ./install_dependencies.sh linux -else - ./install_dependencies.sh osx -fi +# Set c++ to version 11 +export CXXFLAGS="-std=c++11 ${CXXFLAGS}" + 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" .. @@ -15,4 +12,6 @@ if ! ./build/bin/test_validation_suite; then echo "Validation suite failed" >&2 exit 1 fi +cp build/bin/vcf_validator ${PREFIX}/bin +cp build/bin/vcf_assembly_checker ${PREFIX}/bin echo "Done with vcf-validator" diff --git a/recipes/vcf-validator/meta.yaml b/recipes/vcf-validator/meta.yaml index 97f15a68fa213..76476a1844f40 100644 --- a/recipes/vcf-validator/meta.yaml +++ b/recipes/vcf-validator/meta.yaml @@ -1,46 +1,40 @@ {% set name = "vcf-validator" %} -{% set version = "0.9.7" %} +{% set version = "0.10.0" %} package: name: {{ name|lower }} version: {{ version }} source: - git_url: https://github.com/tcezard/vcf-validator.git - git_tag: dynamic_boost -# url: https://github.com/EBIvariation/vcf-validator/archive/refs/tags/v{{ version }}.tar.gz -# sha256: ae0c284dacbe9f15c608d27548d57741ab58f8d7becec6d86bf4b3ef780fa61e + url: https://github.com/EBIvariation/vcf-validator/archive/refs/tags/v{{ version }}.tar.gz + sha256: b46117700445644e6fc5a6d2655b477902c67aba0e7abe8a62df6cb49f923fff build: script: number: 0 - noarch: generic + run_exports: + - {{ pin_subpackage("vcf-validator", max_pin="x.x") }} requirements: host: - - cmake >=2.8 - - sqlite >=3 - - zlib - - automake - - bootstrap - libboost-devel - - libtool - - zstd + - libcurl build: - {{ compiler('c') }} + - {{ compiler('cxx') }} - make - cmake >=2.8 - - sqlite >=3 - - zlib - - automake - - bootstrap - libboost-devel - libtool - zstd - c-ares + - libcurl + - openssl + - bzip2 + - libzlib run: - zstd - + - libcurl test: commands: @@ -54,6 +48,8 @@ about: license_file: LICENSE extra: + additional-platforms: + - osx-arm64 recipe-maintainers: - apriltuesday - tcezard