Merge branch 'bioconda:master' into zamp

bioconda · Oct 16, 2024 · 44efe59 · 44efe59
2 parents f13435a + 0a248ea
commit 44efe59
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diff --git 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:

diff --git 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:

diff --git a/recipes/vcf-validator/LICENSE_ODB b/recipes/vcf-validator/LICENSE_ODB
diff --git 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
@@ -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