Merge remote-tracking branch 'bioconda_origin/master' into saccharis

recipes/augur/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "26.1.0" %}
+{% set version = "26.2.0" %}
 
 package:
   name: augur
   version: {{ version }}
 
 source:
   url: https://github.com/nextstrain/augur/releases/download/{{ version }}/nextstrain_augur-{{ version }}.tar.gz
-  sha256: 74159e9a663ad4f1171b1800dd345dd94777a37dcc74abc754351626f75668c2
+  sha256: a501c10b0242384d33f5fd02ab943d4b295e80f31e2a14b6a9692f01e17ac5af
 
 build:
   number: 0
@@ -33,7 +33,7 @@ requirements:
     - networkx >=2.5,<4
     - numpy >=1.0.0,<2
     - packaging >=19.2
-    - pandas >=1.0.0,<2
+    - pandas >=1.0.0,<3
     - pyfastx >=1.0.0,<3
     - python-calamine >=0.2.0
     - scipy >=1.0.0,<2

recipes/bed2gtf/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "bed2gtf" %}
-{% set version = "1.9.2" %}
+{% set version = "1.9.3" %}
 
 package:
  name: {{ name }}
  version: {{ version }}
 
 source:
  url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v.{{ version }}.tar.gz
- sha256: 38bd7528a5a643a4ade316838af36085809bf6476d1b8f37f126d7678fb7e15f
+ sha256: c6a0b2ea31719932ef6cf002e68d72579daaa327d993da0069b302b51b1b7439
 
 build:
  number: 0

recipes/biobb_gromacs/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "biobb_gromacs" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: dc57bbba78f24fedc9931197fb321428d27078b56b41dd1aafd822c68387cb73
+  sha256: 73c158f537c172c8325d7b6db8748761addf89bf08213aefef66b2a6bd671a3d
 
 build:
   number: 0
@@ -18,13 +18,13 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
     - gromacs ==2022.2
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
     - gromacs ==2022.2
 
 test:

recipes/biobb_haddock/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "biobb_haddock" %}
-{% set version = "4.2.1" %}
+{% set version = "5.0.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: cfd558d0683b3ac9f517aef5c68a801c34efe3d1b6ab948c1a44c3976be5b105
+  sha256: 6a41e63280f577e16e923bc1027967c37a3dfca823cc21803324c6fe33786bb8
 
 build:
   number: 0
@@ -20,10 +20,10 @@ requirements:
   host:
     - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
   run:
     - python >=3.9
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
 
 test:
   imports:

recipes/biobb_io/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "biobb_io" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: e20b38cb73e956eccd0ff61fef5212da2e52cb7c625664794a50f24b7cfbecd3
+  sha256: bcc7edea8abb40e0332ff069931e4db1a9ad6af3cae1a8b09af29d3a6d1572d7
 
 build:
   number: 0
@@ -18,12 +18,12 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
 test:
   imports:
     - biobb_io

recipes/biobb_model/meta.yaml

@@ -1,8 +1,8 @@
 {% set name = "biobb_model" %}
-{% set version = "4.2.3" %}
+{% set version = "5.0.0" %}
 {% set file_ext = "tar.gz" %}
 {% set hash_type = "sha256" %}
-{% set hash_value = "8c4b87ef92331d060700e5b346cddb718b1cc27b79752b1c8ef3583e0dce0927" %}
+{% set hash_value = "6f0cf1302d1b39404a65199e6aa5b9e4435099c2cef7d948253d20837d03d415" %}
 
 package:
   name: '{{ name|lower }}'
@@ -21,15 +21,15 @@ build:
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
-    - biobb_structure_checking >=3.13.4
+    - biobb_common ==5.0.0
+    - biobb_structure_checking >=3.13.5
     - xmltodict
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
-    - biobb_structure_checking >=3.13.4
+    - python >=3.9
+    - biobb_common ==5.0.0
+    - biobb_structure_checking >=3.13.5
     - xmltodict
 test:
   imports:

recipes/biobb_pdb_tools/meta.yaml

@@ -1,30 +1,30 @@
 {% set name = "biobb_pdb_tools" %}
-{% set version = "4.2.0" %}
+{% set version = "5.0.0" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 025d968ba5a5cee692f03d756f0fc474d7dcdec10e2babf150ad10af205aae25
+  sha256: 46cf4312ab7da0bf9491b1bf89677daf6f1163a3163c41d111863cf1baa1bd9a
 
 build:
-  number: 0
+  number: 1
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}
 
 requirements:
   host:
-    - python >=3.8
+    - python >=3.9
     - setuptools
-    - biobb_common ==4.2.0
+    - biobb_common ==5.0.0
     - pdb-tools
   run:
-    - python >=3.8
-    - biobb_common ==4.2.0
+    - python >=3.9
+    - biobb_common ==5.0.0
     - pdb-tools
 test:
   imports:

recipes/clusty/build.sh

@@ -1,10 +1,14 @@
 #!/bin/bash
-#ln -s ${CC} gcc
-#ln -s ${CXX} g++
-#export PATH=$PATH:$(pwd)
+
 uname_S=`uname -s 2>/dev/null || echo not`
 
-if [ "$uname_S" == "Darwin" ]; then make -j${CPU_COUNT}; else make -j${CPU_COUNT} LEIDEN=true; fi
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
+if [[ "$uname_S" == "Darwin" ]]; then
+	make -j"${CPU_COUNT}" CXX="${CXX}" LDFLAGS="${LDFLAGS}";
+else
+	make LEIDEN=true -j"${CPU_COUNT}" CXX="${CXX}" LDFLAGS="${LDFLAGS}";
+fi
 
 install -d "${PREFIX}/bin"
-install clusty "${PREFIX}/bin"
+install -v -m 0755 clusty "${PREFIX}/bin"

recipes/clusty/buildfixes.patch

@@ -0,0 +1,13 @@
+diff --git a/makefile b/makefile
+index 21492fe..009c44f 100644
+--- a/makefile
++++ b/makefile
+@@ -73,7 +73,7 @@ ifeq ($(DYNAMIC_LINK), true)
+ else
+ ifeq ($(uname_S),Darwin)
+     CFLAGS  = -Wall -O3 $(ARCH_FLAGS) -std=c++17 $(DEFINE_FLAGS) $(INCLUDES)
+-    CLINK	= -lm -O3 -std=c++17 $(ABI_FLAGS) -static-libgcc
++    CLINK	= -lm -O3 -std=c++17 $(ABI_FLAGS)
+ else
+     CFLAGS  = -Wall -O3 $(ARCH_FLAGS) -std=c++17 $(DEFINE_FLAGS) $(INCLUDES) -static -Wl,--whole-archive -lpthread -Wl,--no-whole-archive
+     CLINK	= -lm -static -O3 -std=c++17 $(ABI_FLAGS) -Wl,--whole-archive -lpthread -Wl,--no-whole-archive

recipes/clusty/meta.yaml

@@ -1,42 +1,47 @@
-{% set version = "1.1.1" %}
+{% set name = "clusty" %}
+{% set version = "1.1.4" %}
 
 package:
-  name: clusty
+  name: {{ name }}
   version: {{ version }}
 
 build:
   number: 0
   run_exports:
-  - {{ pin_subpackage('clusty', max_pin='x.x.x') }}
+  - {{ pin_subpackage('clusty', max_pin='x') }}
 
 source:
   git_url: https://github.com/refresh-bio/clusty.git
   git_rev: v{{ version }}
+  patches:
+    - buildfixes.patch  # [osx]
 
 requirements:
   build:
     - make
-    - {{ compiler('c') }}
     - {{ compiler('cxx') }}
+    - {{ compiler('c') }}
     - cmake
     - flex
     - bison
 
+test:
+  commands:
+    - clusty > /dev/null
+
 about:
   home: https://github.com/refresh-bio/clusty
   summary: "Clusty is a tool for large-scale data clustering."
-  license: GPL-3
-  license_family: GPL
+  license: GPL-3.0-or-later
+  license_family: GPL3
   license_file: LICENSE
-
-test:
-  commands:
-    - clusty > /dev/null
+  dev_url: https://github.com/refresh-bio/clusty
+  doc_url: "https://github.com/refresh-bio/clusty/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:
     - linux-aarch64
     - osx-arm64
   skip-lints:
     - uses_vcs_url 
-    - missing_hash
+    - missing_hash

recipes/core-snp-filter/build.sh

@@ -1,10 +1,5 @@
 #!/bin/bash -euo
 
-# Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
-# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
-export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="${BUILD_PREFIX}/.cargo"
-
 # build statically linked binary with Rust
 RUST_BACKTRACE=1
 cargo install --verbose --path . --root $PREFIX
-

recipes/core-snp-filter/meta.yaml

@@ -1,21 +1,23 @@
-{% set version = "0.1.1" %}
+{% set version = "0.2.0" %}
 
 package:
   name: core-snp-filter
   version: {{ version }}
 
 source:
   url: https://github.com/rrwick/Core-SNP-filter/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 6ac542524a22c2c66edba69a937ae637a4a1e62105379ba79708ad74187feed9
+  sha256: 5fa0357c4429e52644a9bdd5dfa4be3a3fc6889073f7678ed5a47f8a7f267c3d
 
 build:
-  number: 1
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('core-snp-filter', max_pin="x.x") }}
 
 requirements:
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
-    - rust >=1.39
+    - {{ compiler('rust') }}
     - pkg-config
     - clangdev
     - make

recipes/crabs/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "crabs" %}
-{% set version = "1.0.6" %}
-{% set sha256 = "8cbb930cd34aab5e7b7edca3403686ce9c15fddaf72fcdb7719a336644c22289" %}
+{% set version = "1.0.7" %}
+{% set sha256 = "24c8fe8a1d2dd8b47c4d8818ecdcfd908f10ceafd8c1a21d9f255d10927a3535" %}
 
 package:
   name: {{ name|lower }}

recipes/gencove/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "gencove" %}
-{% set version = "2.24.1" %}
-{% set sha256 = "3c6d3c236dcad933fcb8298a394b84882398a577aa5f8c140ddefeabeb167513" %}
+{% set version = "2.24.2" %}
+{% set sha256 = "036a0b98259e080f8766193c5ff429fa7ffb7a81105bbfb72282572093d5a9dd" %}
 
 package:
   name: {{ name }}

recipes/meryl/0003-align.patch

@@ -0,0 +1,14 @@
+diff --git a/src/utility/src/align/align-ksw2-extz2-sse.C b/src/utility/src/align/align-ksw2-extz2-sse.C
+index d237b48..f96c6fa 100644
+--- a/src/utility/src/align/align-ksw2-extz2-sse.C
++++ b/src/utility/src/align/align-ksw2-extz2-sse.C
+@@ -304,6 +304,8 @@ void ksw_extz2_sse(void *km, int qlen, const uint8_t *query, int tlen, const uin
+ 		kfree(km, mem2); kfree(km, off);
+ 	}
+ }
+-#endif // __SSE2__
+
+ }  //  merylutil::align::ksw2::v1
++
++#endif // __SSE2__
++

recipes/meryl/build.sh

@@ -1,7 +1,14 @@
 #!/bin/bash
 
+set -xe
+
+ARCH_BUILD="-m64 -msse4.1"
+case $(uname -m) in
+    arm64|aarch64) ARCH_BUILD="" ;;
+esac
+
 make -C src BUILD_DIR="$(pwd)" \
 	TARGET_DIR="${PREFIX}" \
 	CXX="${CXX}" \
-	CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \
+	CXXFLAGS="${CXXFLAGS} -O3 -Wno-c++20-extensions -Wno-inline-namespace-reopened-noninline -Wno-format ${ARCH_BUILD} -I${PREFIX}/include" \
 	LDFLAGS="${LDFLAGS} -fopenmp -L${PREFIX}/lib" -j"${CPU_COUNT}"