From 3666cd95a2ee2eab1ae73baa492c1a6484698454 Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 16 Oct 2024 05:44:05 -0400 Subject: [PATCH 1/3] Update msweep to 2.2.1 (#51423) --- recipes/msweep/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/msweep/meta.yaml b/recipes/msweep/meta.yaml index c3f6dfbac8a1b..64708742989df 100644 --- a/recipes/msweep/meta.yaml +++ b/recipes/msweep/meta.yaml @@ -1,6 +1,6 @@ {% set name = "mSWEEP" %} -{% set version = "2.2.0" %} -{% set sha256 = "9f2cbaaa877466a59171a4e74fe26d462657b62ae0e3b464672e44490a6f3d73" %} +{% set version = "2.2.1" %} +{% set sha256 = "16928507cdd62643b1e4d112fbc5757ef27c9d1f42fadfdd5c947894b2614382" %} {% set user = "PROBIC" %} package: From 12bb46468487c8ba8cee7d88c1c2ab2659dd59a6 Mon Sep 17 00:00:00 2001 From: Timothee Cezard Date: Wed, 16 Oct 2024 10:45:26 +0100 Subject: [PATCH 2/3] Update vcf-validator to v0.10.0 (#51421) * Retrieve the prebuilt binaries * Build from source 1 * add default_ext_library_flag * testing with new branch * remove build parameters * Attempt with dynamic libraries on mac osx * Add support for arm64 on OS-X Add additional comment as per review * Update to the latest tag apply fixes for linting --- recipes/vcf-validator/LICENSE_ODB | 71 ------------------------------- recipes/vcf-validator/build.sh | 19 +++++++-- recipes/vcf-validator/meta.yaml | 50 +++++++++++++--------- 3 files changed, 46 insertions(+), 94 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 7a7491a9e1988..1b1bad0e5fa5a 100644 --- a/recipes/vcf-validator/build.sh +++ b/recipes/vcf-validator/build.sh @@ -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; } +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 03877f075b8f4..76476a1844f40 100644 --- a/recipes/vcf-validator/meta.yaml +++ b/recipes/vcf-validator/meta.yaml @@ -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: @@ -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 \ No newline at end of file From 0a248eac47d390664c433be05aefd35c15499cff Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Wed, 16 Oct 2024 06:56:34 -0400 Subject: [PATCH 3/3] Update gempipe to 1.35.5 (#51422) --- recipes/gempipe/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/gempipe/meta.yaml b/recipes/gempipe/meta.yaml index 942b8f4e376b1..5a4202bb38d3e 100755 --- a/recipes/gempipe/meta.yaml +++ b/recipes/gempipe/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.35.4" %} +{% set version = "1.35.5" %} package: name: "gempipe" @@ -7,7 +7,7 @@ package: source: url: https://github.com/lazzarigioele/gempipe/archive/v{{ version }}.tar.gz - sha256: 10bb83284848f8c21baa4069150e65e5a092771b5c5b6396d1e58c33431960a1 + sha256: 748335be2faa39ad12f4cab43a300d98a9c0f51aad4e9cad088eefd1284527e9 build: