Merge branch 'master' into bulk

bioconda · Jan 7, 2025 · 1ee0795 · 1ee0795
2 parents 5791688 + 68539b4
commit 1ee0795
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -97,8 +97,6 @@ recipes/wtforms-components
 recipes/xmlbuilder
 
 # the following packages have open PRs labeled with "Move to conda-forge"
-recipes/perl-alien-build
-recipes/perl-alien-libxml2
 recipes/perl-date-manip
 recipes/perl-datetime-timezone
 recipes/perl-devel-checklib
@@ -118,7 +116,6 @@ recipes/perl-sereal-decoder
 recipes/perl-sereal-encoder
 recipes/perl-term-progressbar
 recipes/perl-uri
-recipes/perl-xml-libxml
 recipes/scoop
 recipes/wheezy.template
 
@@ -607,7 +604,6 @@ recipes/fastuniq
 recipes/fgap
 recipes/funcannot
 recipes/genepender
-recipes/ghostx
 recipes/ls-gkm
 recipes/mosaik
 recipes/ngmerge

diff --git a/recipes/abnumber/meta.yaml b/recipes/abnumber/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "0.4.1" %} # Remember to update sha256 below
+{% set version = "0.4.2" %} # Remember to update sha256 below
 
 package:
   name: abnumber
   version: '{{ version }}'
 
 source:
   url: https://github.com/prihoda/abnumber/archive/v{{ version }}.tar.gz
-  sha256: '240c7ccc1f85607ffdd0109f19761ab0488a059ae15e3ccd6066ef36c192a047'
+  sha256: 'b816fee3db6c018f6963a5e4ce2d23b2889251fb42b7b93d42e81805cd418bc5'
 
 build:
   noarch: python
@@ -19,6 +19,7 @@ requirements:
   host:
     - python >=3.6
     - pip
+    - setuptools
   run:
     - python >=3.6
     - biopython

diff --git a/recipes/alevin-fry/build.sh b/recipes/alevin-fry/build.sh
@@ -2,6 +2,11 @@
 export CFLAGS="${CFLAGS} -fcommon"
 export CXXFLAGS="${CFLAGS} -fcommon"
 
+if [ "$(uname)" == "Darwin" ]; then
+  export CFLAGS="${CFLAGS} -fno-define-target-os-macros"
+  export CXXFLAGS="${CXXFLAGS} -fno-define-target-os-macros"
+fi
+
 # Add workaround for SSH-based Git connections from Rust/cargo.  See https://github.com/rust-lang/cargo/issues/2078 for details.
 # We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct.
 export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo"

diff --git a/recipes/alevin-fry/meta.yaml b/recipes/alevin-fry/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.11.0" %}
+{% set version = "0.11.1" %}
 
 package:
   name: alevin-fry
@@ -11,7 +11,7 @@ build:
 
 source:
   url: https://github.com/COMBINE-lab/alevin-fry/releases/download/v{{ version }}/source.tar.gz
-  sha256: c209a092fd89f37c64bd35679d57d8452c8da7bf75b7b34f8bd5fefcb2703758
+  sha256: c5a35c4b72114b4ef8d1c933cb01e5bb37df47286acd9a78a92f9ae9bf9dd3cf
   #patches:
   #  - use-libradicl-0.8.2.patch
 
@@ -39,4 +39,4 @@ about:
 extra:
   additional-platforms:
     - linux-aarch64
-    - osx-arm
+    - osx-arm64
diff --git a/recipes/alignstats/build.sh b/recipes/alignstats/build.sh
@@ -1,9 +1,11 @@
 #!/bin/bash
 set -eu -o pipefail
 
+export M4="${BUILD_PREFIX}/bin/m4"
 cd "${SRC_DIR}"
 
 autoconf
-./configure --prefix="${PREFIX}"
-make
+autoupdate
+./configure --prefix="${PREFIX}" CC="${CC}"
+make -j"${CPU_COUNT}"
 make install
diff --git a/recipes/alignstats/meta.yaml b/recipes/alignstats/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "0.10" %}
-{% set sha256 = "cc9a11e34889832180aba0e9b01367b7cd0e828c2b667afc9c6ddea8d5928490" %}
+{% set version = "0.11" %}
+{% set sha256 = "8b689b5c3d2d8bf9ea09b319add372dc8acf5b7a30259817ed1ed55ac8505f9e" %}
 
 package:
   name: alignstats
@@ -10,15 +10,16 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 3
+  number: 0
   run_exports:
-    - {{ pin_subpackage("alignstats", max_pin="x.x.x") }}  
+    - {{ pin_subpackage("alignstats", max_pin="x.x") }}  
 
 requirements:
   build:
     - make
     - autoconf
     - automake
+    - libtool
     - {{ compiler('c') }}
   host:
     - htslib >1.4
@@ -39,3 +40,4 @@ about:
 extra:
   additional-platforms:
     - linux-aarch64
+    - osx-arm64
diff --git a/recipes/allhic/build.sh b/recipes/allhic/build.sh
@@ -0,0 +1,9 @@
+#!/usr/bin/env bash
+
+set -xe
+
+go mod tidy
+go build -o allhic -v cmd/main.go
+
+mkdir -p ${PREFIX}/bin
+install -m 755 allhic ${PREFIX}/bin
diff --git a/recipes/allhic/meta.yaml b/recipes/allhic/meta.yaml
@@ -0,0 +1,36 @@
+{% set name = "allhic" %}
+{% set version = "0.9.14" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+source:
+  url: https://github.com/tanghaibao/allhic/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: b73d66d591b69b9456df61e3374b79f86a5501080805f02bc5ea56809d889de5
+
+requirements:
+  build:
+    - {{ compiler('go') }}
+
+test:
+  commands:
+    - allhic --help
+
+about:
+  home: https://github.com/tanghaibao/allhic
+  license: BSD-3-Clause
+  license_family: BSD
+  license_file: LICENSE
+  summary: Genome scaffolding based on HiC data in heterozygous and high ploidy genomes
+  dev_url: https://github.com/tanghaibao/allhic
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
diff --git a/recipes/ampliconsuite/meta.yaml b/recipes/ampliconsuite/meta.yaml
@@ -1,6 +1,6 @@
 {% set name="ampliconsuite" %}
-{% set AS_version="1.3.4" %}
-{% set AA_version="1.4.r2" %}
+{% set AS_version="1.3.5" %}
+{% set AA_version="1.5.r0" %}
 {% set AC_version="1.2.1" %}
 
 package:
@@ -11,9 +11,9 @@ source:
     # the sha256 sum is generated by running the following on the release .tar.gz from Github.
     # $ wget -O- [URL] | shasum -a 256
     - url: https://github.com/AmpliconSuite/AmpliconSuite-pipeline/archive/v{{ AS_version }}.tar.gz
-      sha256: 58f2b74eac0116e0830bceea66a854071e2a205b6f5b8e57ce61a0e358434a61
+      sha256: 6f3fa35435375ae4b76bb9006da9a13e323d633c2e93e06233ca917df6aad3e7
     - url: https://github.com/AmpliconSuite/AmpliconArchitect/archive/v{{ AA_version }}.tar.gz
-      sha256: 987390d7a32a6c118e6c7fea5c7a5aba2db1b3e64fc3ece5f68f50c7cabf01fa
+      sha256: b82dc321ec18238755ab67e2b6e38762c8a0caab77579239b88561f5b9000bbd
       folder: ampliconarchitectlib
     - url: https://github.com/AmpliconSuite/AmpliconClassifier/archive/v{{ AC_version }}.tar.gz
       sha256: 5cd6b9f4e2239631b8f11adda99d8858c29de64cf6f1c7a38121946db06803c9
@@ -44,6 +44,7 @@ requirements:
         - bedtools
     host:
         - python >=3
+        - setuptools
 
 test:
     commands:

diff --git a/recipes/handyreadgenotyper/meta.yaml → recipes/amplicontyper/meta.yaml b/recipes/handyreadgenotyper/meta.yaml → recipes/amplicontyper/meta.yaml
@@ -1,34 +1,36 @@
-{% set name = "HandyReadGenotyper" %}
-{% set version = "0.1.24" %}
+{% set name = "AmpliconTyper" %}
+{% set version = "0.1.28" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://github.com/AntonS-bio/HandyReadGenotyper/archive/{{ version }}.tar.gz
-  sha256: 11970c9bff8b4b7569e7a124030ccc9a0c53a70bb55fe49fcda735857781a731
+  url: https://github.com/AntonS-bio/AmpliconTyper/archive/{{ version }}.tar.gz
+  sha256: 1570c711f0702cc72bda66247086f8d0eafca736101da85d9feaad95dd6600c2
 
 build:
   noarch: python
   script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
   run_exports:
-      - {{ pin_subpackage('handyreadgenotyper', max_pin="x.x") }}  
+      - {{ pin_subpackage('amplicontyper', max_pin="x.x") }}  
   number: 0
 
 requirements:
   host:
     - pip
     - python >=3.10
+    - setuptools
   run:
     - python >=3.10
     - pandas >=2.0.0
-    - scikit-learn >=1.3.*
+    - scikit-learn =1.5.*
     - pysam >=0.22.0
     - numpy >=1.20.*
     - tqdm >=4.66.*
     - biopython >=1.78
     - minimap2
+    - requests
     - samtools
 
 test:
@@ -41,11 +43,11 @@ test:
 about:
   license: GPL-3.0-only
   license_file: LICENSE
-  home: https://github.com/AntonS-bio/HandyReadGenotyper
+  home: https://github.com/AntonS-bio/AmpliconTyper
   summary: 'Tool for training model and classifying reads from environmental ONT amplicon sequencing.'
   description: |
     Tool for training model and classifying reads from environmental ONT amplicon sequencing. 
-  doc_source_url: https://github.com/AntonS-bio/HandyAmpliconTool/blob/main/README.md
+  doc_source_url: https://github.com/AntonS-bio/AmpliconTyper/blob/main/README.md
 
 
 extra:

diff --git a/recipes/annosine2/meta.yaml b/recipes/annosine2/meta.yaml
@@ -10,10 +10,10 @@ source:
   sha256: 94387b895e2b011125211039598b8c426124aa43be6915697243497eefb7fff8
 
 build:
-  number: 0
+  number: 1
   entry_points:
     - AnnoSINE_v2 = AnnoSINE.AnnoSINE_v2:main
-  script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed -vvv "
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   run_exports:
         - {{ pin_subpackage('annosine2', max_pin="x") }}
   noarch: python
@@ -42,18 +42,20 @@ requirements:
     - repeatmasker
     - seqtk
 
-
 test:
   imports:
     - AnnoSINE
   commands:
     - AnnoSINE_v2 --help
 
 about:
-  home: https://github.com/liaoherui/AnnoSINE_v2
+  home: "https://github.com/liaoherui/AnnoSINE_v2"
   license: MIT
   license_family: MIT
-  summary: AnnoSINE_v2 - SINE Annotation Tool for Plant and Animal Genomes
+  license_file: LICENSE
+  summary: "AnnoSINE_v2 - SINE Annotation Tool for Plant and Animal Genomes."
+  dev_url: "https://github.com/liaoherui/AnnoSINE_v2"
+  doc_url: "https://github.com/liaoherui/AnnoSINE_v2/blob/main/README.md"
 
 extra:
   recipe-maintainers:

diff --git a/recipes/artic/meta.yaml b/recipes/artic/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "artic" %}
-{% set version = "1.5.7" %}
-{% set sha256 = "fa98d6c15797f9e4394fa3ee1b31ad7fab596280c20f806888013b2f6f849057" %}
+{% set version = "1.6.0" %}
+{% set sha256 = "9037ce813170e76ee2e37b94871b549e850faad26fffab201c04a2368ab81cfc" %}
 
 package:
   name: {{ name|lower }}
@@ -52,6 +52,7 @@ requirements:
     - requests
     - samtools
     - tqdm
+    - seqtk
 
 test:
   commands:

diff --git a/recipes/bakta/meta.yaml b/recipes/bakta/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "1.10.2" %}
+{% set version = "1.10.3" %}
 
 package:
   name: bakta
   version: '{{ version }}'
 
 source:
   url: https://github.com/oschwengers/bakta/archive/v{{ version }}.tar.gz
-  sha256: 'ed0b9821c740d11c494009bb2c395a5c8b9903e8b04b3abf9c465ca45b0ef739'
+  sha256: '99ee0bcf559fabcebb3c1e896638da537a0691312eb07fd41788f3cb79ef22ba'
 
 build:
   noarch: python

diff --git a/recipes/beagle-lib/3.1.2/build.sh b/recipes/beagle-lib/3.1.2/build.sh
@@ -0,0 +1,24 @@
+#!/bin/bash
+
+set -xe
+
+export M4="${BUILD_PREFIX}/bin/m4"
+export INCLUDES="-I{PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CFLAGS="${CFLAGS} -O3"
+export CXXFLAGS="${CXXFLAGS} -O3"
+
+case $(uname -m) in
+	aarch64 | arm64)
+		ARCH_OPTS="--disable-sse"
+		;;
+	*)
+		ARCH_OPTS=""
+		;;
+esac
+
+./autogen.sh
+./configure CC="${CC}" CXX="${CXX}" --prefix=${PREFIX} --with-jdk=${PREFIX} --disable-march-native ${ARCH_OPTS}
+make -j ${CPU_COUNT}
+make install