Merge branch 'master' into r-pgenlibr

recipes/bam2plot/meta.yaml

@@ -0,0 +1,48 @@
+{% set name = "bam2plot" %}
+{% set version = "0.3.6" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/bam2plot-{{ version }}.tar.gz
+  sha256: 7be991b42db59d0c06ca2f354f906238be3c4f4d0588d85dd1cfd1ec7752a541
+
+build:
+  entry_points:
+    - bam2plot=bam2plot.main:cli
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('bam2plot', max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.10
+    - pip
+    - setuptools
+  run:
+    - python >=3.10
+    - pysam >=0.22.0
+    - seaborn >=0.13.2
+    - polars >=0.20.15
+    - mappy >=2.28
+    - pyfastx
+    - pyarrow
+    - mosdepth
+
+test:
+  imports:
+    - bam2plot
+  commands:
+    - bam2plot from_bam --help
+    - bam2plot from_reads --help
+    - bam2plot guci --help
+
+about:
+  home: https://github.com/willros/bam2plot
+  summary: Plot of coverage from bam file
+  license: GPL-3.0-only
+  license_file: LICENSE

recipes/biobb_chemistry/meta.yaml

@@ -1,16 +1,16 @@
 {% set name = "biobb_chemistry" %}
-{% set version = "5.0.1" %}
+{% set version = "5.0.2" %}
 
 package:
   name: '{{ name|lower }}'
   version: '{{ version }}'
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 585effae00b36a8ace8171c399b99afc9bf8103770caf341b6bff7ba7df1ee88
+  sha256: 96c42dda4f898413f3430c6cf73e14f4ab171a93cb8c1faa266f0ded2f905b05
 
 build:
-  number: 0
+  number: 1
   noarch: python
   script: "{{ PYTHON }} -m pip install . --no-deps --ignore-installed --no-cache-dir -vvv"
   run_exports:
@@ -22,13 +22,13 @@ requirements:
     - setuptools
     - biobb_common ==5.0.0
     - openbabel ==3.1.1
-    - ambertools <=22.5
+    - ambertools ==22.5
     - acpype >=2023.10.27
   run:
     - python >=3.9
     - biobb_common ==5.0.0
     - openbabel ==3.1.1
-    - ambertools <=22.5
+    - ambertools ==22.5
     - acpype >=2023.10.27
 test:
   imports:

recipes/bioblend/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "bioblend" %}
-{% set version = "1.3.0" %}
+{% set version = "1.4.0" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/b/bioblend/bioblend-{{ version }}.tar.gz
-  sha256: e72318e10c29a81c16281d25aaac00989a07fc2900be7479137964232cc4a507
+  sha256: 175d49d288e27d132ff59c870551c87cd95d7747be55ab94807c563291a3fa1d
 
 build:
   number: 0
@@ -22,6 +22,7 @@ requirements:
   host:
     - python >=3.8
     - pip
+    - setuptools
   run:
     - python >=3.8
     - requests >=2.20.0
@@ -66,7 +67,7 @@ test:
 about:
   home: "https://github.com/galaxyproject/bioblend"
   license: MIT
-  summary: 'A Python library for interacting with the Galaxy API'
+  summary: 'A Python library for interacting with the Galaxy API.'
   license_family: MIT
   license_file: LICENSE
   doc_url: "https://bioblend.readthedocs.org/"

recipes/centrifuger/meta.yaml

@@ -1,18 +1,18 @@
 {% set name = "centrifuger" %}
-{% set version = "1.0.4" %}
+{% set version = "1.0.5" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
 source:
   url: https://github.com/mourisl/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 5261abcfb3b88126000ae7708702d07704a0ee19d6f54f9f89f0d2e195e24d1d
+  sha256: 1de388229d3ee6a65a58308b5521bef6cbfcdf92628064a39d6b70c7523d68de
 
 requirements:
   build:

recipes/dxpy/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "dxpy" %}
-{% set version = "0.384.0" %}
+{% set version = "0.385.0" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 17e29e9f58843c2639d53ea02b0dfd5c9940ad4ff20ab9e4df895a664f07e392
+  sha256: 6e0d06e9704e9845967caaf301e918496056ad58e15bd610fb02c3c4d775adcf
 
 build:
   number: 0

recipes/evofr/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "0.1.23" %}
+{% set version = "0.1.25" %}
 
 package:
   name: evofr
   version: {{ version }}
 
 source:
   url: https://pypi.io/packages/source/e/evofr/evofr-{{ version }}.tar.gz
-  sha256: ac159419119c000e403b5801d8b6dfef215bcbeca6f30f3bf13b66b90b64ad17
+  sha256: 7360736349cad3a665acc80f4e6d3c4fe205a991dae2e35ab86d56b66214bf30
 
 build:
   number: 0

recipes/fastp/meta.yaml

@@ -1,15 +1,15 @@
-{% set version="0.23.4" %}
+{% set version="0.24.0" %}
 
 package:
   name: fastp
   version: {{ version }}
 
 source:
   url: https://github.com/OpenGene/fastp/archive/v{{ version }}.tar.gz
-  sha256: 4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5
+  sha256: 42445973c57be9209c753027e99781261c69381013813c576ad447e413ff3d04
 
 build:
-  number: 5
+  number: 0
   run_exports:
     - {{ pin_subpackage("fastp", max_pin="x.x") }}
 

recipes/gadma/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "gadma" %}
-{% set version = "2.0.0" %}
+{% set version = "2.0.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: 1e891b87749261ce9c1866fd3e0ac389306096e3b940eb364101448efeca4cfd
+  sha256: f7b610d0d347e97afb30e6b5f9a814c19e479203838de31aa2e44f7427073db5
 
 build:
   number: 0
@@ -19,27 +19,31 @@ build:
     - gadma-get_confidence_intervals = gadma.get_confidence_intervals:main
     - gadma-get_confidence_intervals_for_ld = gadma.get_confidence_intervals_for_ld:main
     - gadma-precompute_ld_data = gadma.precompute_ld_data:main
-  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation -vvv"
+  script: "{{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv"
   noarch: python
   run_exports:
     - {{ pin_subpackage('gadma', max_pin="x") }}
 
 requirements:
   host:
-    - python >=3.6,<3.9
+    - python >=3.6
     - pip
     - setuptools-scm
+    - setuptools
   run:
-    - python >=3.6,<3.9
+    - python >=3.6
     - dadi
+    - demes
+    - demesdraw
+    - h5py ==3.10.0
     - matplotlib-base
     - mpmath
     - nlopt
     - numpy
-    - pandas
+    - pandas <=2.2.2
     - pillow
-    - ruamel.yaml
-    - scipy
+    - ruamel.yaml ==0.16.12
+    - scipy <1.14
     - networkx
     - moments
     - scikit-allel
@@ -69,6 +73,7 @@ about:
   license_file: LICENSE
   summary: "Genetic Algorithm for Demographic Inference"
   doc_url: https://gadma.readthedocs.io/en/latest/
+  dev_url: "https://github.com/ctlab/GADMA"
 
 extra:
   identifiers:

recipes/gencove/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "gencove" %}
-{% set version = "2.24.0" %}
-{% set sha256 = "1ec41ae1e663d7ab27b3c1e6af3eccb49e95120d084bae4c25305aab1126e7fb" %}
+{% set version = "2.24.1" %}
+{% set sha256 = "3c6d3c236dcad933fcb8298a394b84882398a577aa5f8c140ddefeabeb167513" %}
 
 package:
   name: {{ name }}

recipes/gnparser/meta.yaml

@@ -1,5 +1,5 @@
-{% set version = "1.10.3" %}
-{% set sha256 = "899661ab88b716b7c1e3c4430bfb388997e510b28961e0246c361407f34cf0d2" %}
+{% set version = "1.10.4" %}
+{% set sha256 = "55e944b38dab4c680e96fd5b0effc2ccef300e91da1b6076cea4ad4e4e93fbcb" %}
 
 package:
   name: "gnparser"
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('gnparser', max_pin="x") }}
 

recipes/goldrush/meta.yaml

@@ -11,7 +11,7 @@ source:
 
 build:
   skip: true  # [py < 38 or win or py > 39]
-  number: 0
+  number: 1
   run_exports: {{ pin_subpackage("goldrush", max_pin="x") }}
 
 requirements:
@@ -41,6 +41,7 @@ requirements:
     - gperftools
     - bc
     - snakemake
+    - numpy >=1.22.4
 
 test:
   commands:

recipes/halfdeep/build.sh

@@ -0,0 +1,28 @@
+#!/usr/bin/env bash
+
+set -o errexit
+set -o nounset
+set -o xtrace
+
+mkdir -vp "${PREFIX}/bin"
+
+# Define installation manifest
+declare -A files=(
+    ["bam_depth.sh"]="0755"
+    ["halfdeep.sh"]="0755"
+    ["halfdeep.r"]="0755"
+    ["scaffold_lengths.py"]="0755"
+)
+
+# Install files
+for file in "${!files[@]}"; do
+    if [[ ! -f "$SRC_DIR/$file" ]]; then
+        echo "Source file $file not found in $SRC_DIR" >&2
+        exit 1
+    fi
+
+    if ! install -v -m "${files[$file]}" "$SRC_DIR/$file" "$PREFIX/bin/$file"; then
+        echo "Failed to install $file" >&2
+        exit 1
+    fi
+done

recipes/halfdeep/meta.yaml

@@ -0,0 +1,41 @@
+{% set name = "HalfDeep" %}
+{% set version = "0.1.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/richard-burhans/{{ name }}/archive/refs/tags/{{ version }}.zip
+  sha256: 308341c567298703fb99d4ceac7b34f0718cf6a37b02fc166f68d661a7f44f27
+
+requirements:
+  run:
+    - bash
+    - coreutils
+    - gawk
+    - genodsp
+    - grep
+    - gzip
+    - minimap2
+    - python >={{ python_min | default("3.9") }}
+    - r-base >={{ r_base | default("4.3.*") }}
+    - samtools
+    - sed
+
+build:
+  number: 0
+  noarch: generic
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin="x.x") }}
+
+test:
+  commands:
+    - ${PREFIX}/bin/genodsp --help
+
+about:
+  home: https://github.com/richard-burhans/{{ name }}
+  summary: Automated detection of intervals covered at half depth by sequenced reads.
+  license: BSD-3-Clause
+  license_file: LICENSE
+  license_url: https://github.com/richard-burhans/{{ name }}/blob/master/LICENSE