From 0ceb8f65d3aac73681f4942570526274358811f8 Mon Sep 17 00:00:00 2001
From: Xi Zhang <13602037587@163.com>
Date: Fri, 27 Sep 2024 23:59:15 -0600
Subject: [PATCH 01/26] update Hsdecipher des (#51023)

---
 recipes/hsdecipher/meta.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/recipes/hsdecipher/meta.yaml b/recipes/hsdecipher/meta.yaml
index 1c09c04b459a4..e03d9d9cfca9c 100644
--- a/recipes/hsdecipher/meta.yaml
+++ b/recipes/hsdecipher/meta.yaml
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://github.com/zx0223winner/{{name|lower}}_conda/archive/refs/tags/v{{version}}.tar.gz
-  sha256: ea5eec38927972070d65d126d410b6059ef0d1d8ef8fa5db23fa045c5e749543
+  sha256: 54ab84f8584c69a50db4678b49279b0a0b4b05cf0028eec9c2f2ea2205917b76
 
 build:
-  number: 0
+  number: 1
   noarch: python
   script: bash conda_build_package.sh
   run_exports:
@@ -24,10 +24,11 @@ requirements:
     - matplotlib-base
 test:
   commands:
-    - hsd_heatmap -h
+    - hsdecipher -h
 about:
   home: https://github.com/zx0223winner/HSDecipher
   summary: Pipeline for the downstream analysis of highly similar duplicate genes
+  description: "Many tools have been developed to measure the degree of similarity between gene duplicates within and between species.Here, we present HSDecipher, a bioinformatics pipeline to assist users in the analysis and visualization of highly similar duplicate genes (HSDs). We describe the steps for analysis of HSDs statistics, expanding HSD gene set, and visualizing the results of comparative genomic analyses. HSDecipher represents a useful tool for researchers exploring the evolution of duplicate genes in select eukaryotic species."
   license: GPL-3.0-or-later
-  license_file: licence
+  license_file: license
 

From bef36ce12d953b064845a462213e65dbf680e4fa Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 28 Sep 2024 16:05:58 -0400
Subject: [PATCH 02/26] Update parsnp to 2.0.6 (#51028)

---
 recipes/parsnp/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/parsnp/meta.yaml b/recipes/parsnp/meta.yaml
index d99dc6f3bfb79..893029bbcf967 100644
--- a/recipes/parsnp/meta.yaml
+++ b/recipes/parsnp/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.0.5" %}
+{% set version = "2.0.6" %}
 
 package:
   name: parsnp
@@ -6,7 +6,7 @@ package:
 
 source:
   url: "https://github.com/marbl/parsnp/archive/refs/tags/v{{version}}.tar.gz"
-  sha256: 1d23695d0d624fa17e02c43b1d730200e526c17a48615593f75ee8fc35402489
+  sha256: cde5fb488418764e87942afa747002d01d35e80d7c3a44a71bb2d1bd4d69ed0c
 
 build:
   number: 0

From 777cf9c7c420d19327d1c3c172ea24967e747c84 Mon Sep 17 00:00:00 2001
From: Eric Roberts <notthebmovieactor@gmail.com>
Date: Sat, 28 Sep 2024 21:07:44 -0400
Subject: [PATCH 03/26] Fix path.py package renaming to path for Genomedata
 recipe (#51022)

---
 recipes/genomedata/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/genomedata/meta.yaml b/recipes/genomedata/meta.yaml
index 5959be0568f95..12a66928b7dc5 100644
--- a/recipes/genomedata/meta.yaml
+++ b/recipes/genomedata/meta.yaml
@@ -12,7 +12,7 @@ source:
 
 build:
   skip: True  # [osx or py < 39]
-  number: 0
+  number: 1
   entry_points:
     - genomedata-close-data = genomedata._close_data:main
     - genomedata-erase-data = genomedata._erase_data:main
@@ -45,7 +45,7 @@ requirements:
     - hdf5
     - pytables >=3.4.3
     - pybigwig
-    - path.py
+    - path
     - textinput
     - bedtools
     - ucsc-bigwigtobedgraph >=377

From 0add3f58634ec2dfb5346886d239511d4206194c Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sat, 28 Sep 2024 21:15:37 -0400
Subject: [PATCH 04/26] Update quatradis to 1.3.1 (#51027)

---
 recipes/quatradis/meta.yaml | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/recipes/quatradis/meta.yaml b/recipes/quatradis/meta.yaml
index a91fb4a8cd361..d06896d5b8edc 100644
--- a/recipes/quatradis/meta.yaml
+++ b/recipes/quatradis/meta.yaml
@@ -1,4 +1,4 @@
-{% set version="1.3.0" %}
+{% set version = "1.3.1" %}
 
 package:
   name: quatradis
@@ -6,33 +6,32 @@ package:
 
 source:
   url: https://github.com/quadram-institute-bioscience/QuaTradis/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 8634c61c93073028fc35df46b3d1337e7716924051c336a12172c65e1adb2e74
+  sha256: 0c05f40e14391b5044aa014cce345e43238ff01d06edfc72258f8608d3796590
 
 build:
   number: 0
-  script: python -m pip install -v --no-deps --ignore-installed .
+  script: {{ PYTHON }} -m pip install -vvv --no-deps --no-build-isolation --no-cache-dir .
   run_exports:
-    - {{ pin_subpackage('quatradis', max_pin="x.x") }}
+    - {{ pin_subpackage('quatradis', max_pin="x") }}
     
 requirements:
   build:
     - {{ compiler('c') }}
   host:
-    - python =3.10
-    - cython >=0.20.1
+    - python
+    - cython
     - pip
   run:
-    - python =3.10
-    - cython
+    - python
     - setuptools  # for pkg_resources
+    - cython
     - biopython
     - pysam >=0.18.0
     - matplotlib-base
     - numpy
     - scipy
-    - dendropy
-    - seaborn
-    - graphviz
+    - dendropy ==4.6
+    - seaborn-base
     - python-graphviz
     - pandas
     - htslib
@@ -43,7 +42,7 @@ requirements:
     - bwa
     - samtools
     - minimap2
-    - snakemake
+    - snakemake-minimal
     - snakeviz
         
 test:
@@ -56,6 +55,7 @@ about:
   license_family: GPL3
   license_file: LICENSE
   summary: 'A set of tools to analyse the output from TraDIS analyses'
+  dev_url: https://github.com/quadram-institute-bioscience/QuaTradis
 
 extra:
   skip-lints:
@@ -66,5 +66,5 @@ extra:
     - sbastkowski
     - maplesond
     - thanhleviet
-  doi:
-    - 10.1093/bioinformatics/btw022
+  identifiers:
+    - doi:10.1093/bioinformatics/btw022

From 99d5150b501a59690ca25f488d403421332498d7 Mon Sep 17 00:00:00 2001
From: Jaebeom Kim <68528165+jaebeom-kim@users.noreply.github.com>
Date: Mon, 30 Sep 2024 02:13:15 +0900
Subject: [PATCH 05/26] Update: Metabuli 1.0.8 (#51030)

---
 recipes/metabuli/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/metabuli/meta.yaml b/recipes/metabuli/meta.yaml
index 0d6ed66393dbf..474fe1ebaeca8 100644
--- a/recipes/metabuli/meta.yaml
+++ b/recipes/metabuli/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "1.0.5" %}
-{% set sha256 = "c84a4e2436904f0cbea7126abf2a5f665a870735c8af786883e10f3f872bda28" %}
+{% set version = "1.0.8" %}
+{% set sha256 = "cc7e496ff82f00b56ef59aa2a04fa572a2025225b0558e0df144f166fade82d4" %}
 
 package:
   name: metabuli
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('metabuli', max_pin="x") }}
 

From 20c248d66c43d820bf4fdaed54f0f2dcaa4e3a47 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sun, 29 Sep 2024 13:15:10 -0400
Subject: [PATCH 06/26] Update gxf2bed to 0.2.3 (#51029)

---
 recipes/gxf2bed/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/gxf2bed/meta.yaml b/recipes/gxf2bed/meta.yaml
index a0b0d0160416c..61af4d475731e 100644
--- a/recipes/gxf2bed/meta.yaml
+++ b/recipes/gxf2bed/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "gxf2bed" %}
-{% set version = "0.2.2" %}
+{% set version = "0.2.3" %}
 
 package:
   name: gxf2bed
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/alejandrogzi/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: ee500e08e8c94b2663ea511482d6520300cb81c9cbbb05a288563e4a808f5377
+  sha256: 1f8358a972bded0c4906bf03532ba4ee9f7fc6bf9b84063e4b25b98f37ced45f
 
 build:
   number: 0

From 59ef264dd3aa54283e4a15d275947e1c158e4920 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sun, 29 Sep 2024 13:16:10 -0400
Subject: [PATCH 07/26] Update nanovar to 1.8.1 (#51032)

---
 recipes/nanovar/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/nanovar/meta.yaml b/recipes/nanovar/meta.yaml
index 2f73c6d289332..1e0dbbfc3bd97 100644
--- a/recipes/nanovar/meta.yaml
+++ b/recipes/nanovar/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.8.0" %}
+{% set version = "1.8.1" %}
 
 package:
   name: nanovar
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/n/nanovar/nanovar-{{ version }}.tar.gz
-  sha256: 966117fc5667639dee4910823481037dc451ee972b3afdf93786f3f736eb120b
+  sha256: c75159f86a4043f5ba37c4ea16b9c5953e44d7a1c1dd854de7928464bed83bc9
 
 build:
   skip: True  # [py2k or osx or py > 39]
@@ -23,7 +23,7 @@ requirements:
     - python
   run:
     - python
-    - numpy >=1.17.3
+    - numpy >=1.17.3, <2.0.0
     - scipy >=1.2.1
     - biopython >=1.82
     - pybedtools >=0.8.2

From 75dca3f962dcdb50f69fae06f6b4c65c2e319f75 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sun, 29 Sep 2024 13:48:09 -0400
Subject: [PATCH 08/26] Update ont-modkit to 0.4.1 (#51025)

---
 recipes/ont-modkit/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/ont-modkit/meta.yaml b/recipes/ont-modkit/meta.yaml
index 9f45eb5a76e54..f6a36fb5d4699 100644
--- a/recipes/ont-modkit/meta.yaml
+++ b/recipes/ont-modkit/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "ont-modkit" %}
-{% set version = "0.4.0" %}
-{% set sha256 = "a4a304f00f350074b50fb3c71ab8756df0344e0f77a55c443aa48a91c42195bf" %}
+{% set version = "0.4.1" %}
+{% set sha256 = "45cd7d4ee69092db7412a15f02799c3118bf5fa4e40e193e30e8c65c4f762f79" %}
 
 package:
   name: {{ name }}

From f0b880c30d03e11e3285d846f59e4ee5cb58f8d9 Mon Sep 17 00:00:00 2001
From: "Robert A. Petit III" <robbie.petit@gmail.com>
Date: Sun, 29 Sep 2024 17:31:38 -0600
Subject: [PATCH 09/26] add recipe for sizemeup (#51033)

* add recipe for sizemeup

* fix issue on release side

* Update meta.yaml

* reduce python constraint
---
 recipes/sizemeup/build.sh  | 14 +++++++++++
 recipes/sizemeup/meta.yaml | 48 ++++++++++++++++++++++++++++++++++++++
 2 files changed, 62 insertions(+)
 create mode 100644 recipes/sizemeup/build.sh
 create mode 100644 recipes/sizemeup/meta.yaml

diff --git a/recipes/sizemeup/build.sh b/recipes/sizemeup/build.sh
new file mode 100644
index 0000000000000..98412cd73fb29
--- /dev/null
+++ b/recipes/sizemeup/build.sh
@@ -0,0 +1,14 @@
+#!/bin/bash
+
+mkdir -p $PREFIX/bin ${PREFIX}/share/sizemeup
+
+# Install sizemup library
+$PYTHON -m pip install --no-deps --ignore-installed -vv .
+
+# move main executable, and replace with wrapper
+chmod 755 bin/sizemeup-bioconda
+mv $PREFIX/bin/sizemeup $PREFIX/bin/sizemeup-main
+cp -f bin/sizemeup-bioconda $PREFIX/bin/sizemeup
+
+# Copy genome size database (~100kb)
+cp -f data/sizemeup-sizes.txt ${PREFIX}/share/sizemeup
diff --git a/recipes/sizemeup/meta.yaml b/recipes/sizemeup/meta.yaml
new file mode 100644
index 0000000000000..990ed7e6a9e3d
--- /dev/null
+++ b/recipes/sizemeup/meta.yaml
@@ -0,0 +1,48 @@
+{% set name = "sizemeup" %}
+{% set version = "1.0.2" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/rpetit3/sizemeup/archive/v{{ version }}.tar.gz
+  sha256: 0290d945909e20ccd417e4a874c22e14f5904695586974a98424dd9890bc9550
+
+build:
+  number: 0
+  noarch: generic
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  host:
+    - python >=3.7
+    - poetry
+    - pip
+  run:
+    - python >=3.7
+    - requests
+    - rich-click >=1.6.0
+
+test:
+  imports:
+    - sizemeup
+  commands:
+    - pip check
+    - sizemeup --version
+    - sizemeup --help
+    - sizemeup --species "Staphylococcus aureus"
+    - sizemeup-build --help
+  requires:
+    - pip
+
+about:
+  home: https://github.com/rpetit3/sizemeup
+  summary: A simple tool to determine the genome size of an organism
+  license: MIT
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - rpetit3

From 7fb1079ebecc7cf883dcc4a23861a59c7ae96627 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Sun, 29 Sep 2024 23:16:48 -0400
Subject: [PATCH 10/26] Update gtotree to 1.8.7 (#51036)

---
 recipes/gtotree/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/gtotree/meta.yaml b/recipes/gtotree/meta.yaml
index 6955b5089cf72..3adba0cd806f8 100644
--- a/recipes/gtotree/meta.yaml
+++ b/recipes/gtotree/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "GToTree" %}
-{% set version = "1.8.6" %}
+{% set version = "1.8.7" %}
 
 package:
   name: "{{ name|lower }}"
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/AstrobioMike/GToTree/archive/v{{ version }}.tar.gz
-  sha256: 1712d9e18f128bbeeb585b1528a8e207c3a36cc7f1dbb7df66416ec0278d5a9a
+  sha256: 2ec94fa0bbcfa98edca126ee3446ab7fa8982cd746604b371f74a125e3e44435
 
 build:
   number: 0

From bb3073b6bf7d752b6532ce76eb769b45fd7b1f97 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 00:37:18 -0400
Subject: [PATCH 11/26] Update blaze2 to 2.5.0 (#51034)

---
 recipes/blaze2/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/blaze2/meta.yaml b/recipes/blaze2/meta.yaml
index 329bd464af823..098c5e8149ec3 100644
--- a/recipes/blaze2/meta.yaml
+++ b/recipes/blaze2/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "BLAZE2" %}
-{% set version = "2.4.0" %}
+{% set version = "2.5.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/shimlab/BLAZE/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: b4487873d1f4ae389feed54aa7d862ff3addc458c387d6fd0e3c9550c0a2037d
+  sha256: f47175997742562add1deb9524e468b6709e40c92f74165a1a0fe1897b2919fc
 
 build:
   number: 0

From 2092e27da20e8900ce05be73a85e11faff317d9a Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 03:10:59 -0400
Subject: [PATCH 12/26] Update bactopia-teton to 1.0.5 (#51037)

* Update bactopia-teton to 1.0.5

* Update meta.yaml

---------

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
---
 recipes/bactopia-teton/meta.yaml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/recipes/bactopia-teton/meta.yaml b/recipes/bactopia-teton/meta.yaml
index d1b1ab3117925..4319a50a89122 100644
--- a/recipes/bactopia-teton/meta.yaml
+++ b/recipes/bactopia-teton/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.4" %}
+{% set version = "1.0.5" %}
 
 package:
   name: bactopia-teton
@@ -12,7 +12,7 @@ build:
 
 source:
   url: https://github.com/bactopia/bactopia-teton/archive/v{{version}}.tar.gz
-  sha256: 648b476bcf15bc177df1a814d782d318ee6b78a38e2ccb8268c569cbd1576504
+  sha256: 4340da1ca721850564dcc05491ee396d1f9a1bbf662de5ede12fa29c50c1f3be
 
 requirements:
   run:
@@ -28,6 +28,7 @@ requirements:
     - pigz
     - python >=3.6,<3.11
     - sed
+    - sizemeup >=1.0.2
     - sra-human-scrubber >=2.2
 
 test:

From 29062432cd78be85dccbe6bef9c838c2167c5e3c Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 05:00:48 -0400
Subject: [PATCH 13/26] Update r-diffcorr to 0.4.4 (#51039)

---
 recipes/r-diffcorr/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/r-diffcorr/meta.yaml b/recipes/r-diffcorr/meta.yaml
index 75a7764de28b5..71a4ef28bc8e3 100644
--- a/recipes/r-diffcorr/meta.yaml
+++ b/recipes/r-diffcorr/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = '0.4.3' %}
+{% set version = '0.4.4' %}
 
 package:
   name: r-diffcorr
@@ -8,7 +8,7 @@ source:
   url:
     - {{ cran_mirror }}/src/contrib/DiffCorr_{{ version }}.tar.gz
     - {{ cran_mirror }}/src/contrib/Archive/DiffCorr/DiffCorr_{{ version }}.tar.gz
-  sha256: b0d811cbd78eb69484fb184522cc358d9ad56235b85ee56bef22fc3c1d2df3f3
+  sha256: c729fe399aceaf3afb975777ff3483e5d557d9b55b33fe5803bdb8949ff33b17
 
 build:
   number: 0

From c69d1bb2f6189e47d377d921a90baaea4badc992 Mon Sep 17 00:00:00 2001
From: Florian Zwagemaker <49153065+florianzwagemaker@users.noreply.github.com>
Date: Mon, 30 Sep 2024 11:02:34 +0200
Subject: [PATCH 14/26] deps: update mamba versions in recipe and bump build
 number (#51038)

---
 recipes/viroconstrictor/meta.yaml | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/recipes/viroconstrictor/meta.yaml b/recipes/viroconstrictor/meta.yaml
index 40710eace6abf..d3bce9d30f325 100644
--- a/recipes/viroconstrictor/meta.yaml
+++ b/recipes/viroconstrictor/meta.yaml
@@ -17,7 +17,7 @@ build:
     - viroConstrictor = ViroConstrictor.__main__:main
     - Viroconstrictor = ViroConstrictor.__main__:main
   script: {{ PYTHON }} -m pip install . --no-deps -vvv
-  number: 0
+  number: 1
   run_exports:
     - {{ pin_subpackage('viroconstrictor', max_pin="x") }}
 
@@ -40,7 +40,7 @@ requirements:
     - snakemake >=7.15.2, < 8
     - aminoextract ==0.3.1
     - conda
-    - mamba
+    - mamba >=1.5.0, <2.0.0
 
 test:
   imports:
@@ -63,5 +63,6 @@ about:
 extra:
   recipe-maintainers:
     - florianzwagemaker
-    - KHajji
+    - raaijmag
+    - wolthuisr
     - ids-bioinformatics

From 141a0305cad4044cd4926179f8f46da67bed5f42 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 05:51:00 -0400
Subject: [PATCH 15/26] Update agfusion to 1.4.3 (#51041)

---
 recipes/agfusion/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/agfusion/meta.yaml b/recipes/agfusion/meta.yaml
index 8aa1ba254810a..e75269053c624 100644
--- a/recipes/agfusion/meta.yaml
+++ b/recipes/agfusion/meta.yaml
@@ -1,5 +1,5 @@
-{% set version = "1.4.1" %}
-{% set sha256 = "fd04591d764deeff69978f9d495c3baf854ccfba27366aa0ae4859ad85ca2c60" %}
+{% set version = "1.4.3" %}
+{% set sha256 = "0fdace7fad64713173cac049af3783bdb3db406d5a6dafd4cc0c1948d0724c8f" %}
 
 package:
   name: agfusion

From 5fec5ff1b6cfb9d9cc0130192b06132cb6a5a899 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 09:22:58 -0400
Subject: [PATCH 16/26] Update slow5tools to 1.3.0 (#51048)

---
 recipes/slow5tools/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/slow5tools/meta.yaml b/recipes/slow5tools/meta.yaml
index 1886640a6b95d..4941e1c8f1dc6 100644
--- a/recipes/slow5tools/meta.yaml
+++ b/recipes/slow5tools/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "slow5tools" %}
-{% set version = "1.2.0" %}
+{% set version = "1.3.0" %}
 
 package:
   name: {{ name }}
@@ -7,10 +7,10 @@ package:
 
 source:
   url: https://github.com/hasindu2008/slow5tools/releases/download/v{{ version }}/slow5tools-v{{ version }}-release.tar.gz
-  sha256: ce9d198f8368e90f440fce974e798b7f521b0fe4f859caf9a452bba1ca5af2d4
+  sha256: f7221285e0090a5ca05a75f5e70c51d093138b2c8ad658b2756c3c6e51097d5d
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage('slow5tools', max_pin="x") }}
 

From 3aeafb0f5d5cae7393b3b8b3626ee270e4b2e95a Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 09:23:23 -0400
Subject: [PATCH 17/26] Update seqfu to 1.22.2 (#51047)

* Update seqfu to 1.22.1

* Update seqfu to 1.22.2
---
 recipes/seqfu/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/seqfu/meta.yaml b/recipes/seqfu/meta.yaml
index f101b83e34093..9dfcd4bb28b7f 100644
--- a/recipes/seqfu/meta.yaml
+++ b/recipes/seqfu/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "seqfu" %}
-{% set version = "1.22.0" %}
-{% set sha256 = "e1b9032caab8e2effcc5a075b372c2fae636494b06e3bf2f30086c8d39fb5281" %}
+{% set version = "1.22.2" %}
+{% set sha256 = "0b66405ca98a80be614874fd1c1f651ecb410d953ac5070a0e93c77d2dbe1919" %}
 
 package:
   name: {{ name }}

From e6cdc8b5a0e6b857972f239857ed796ad097768a Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 09:33:49 -0400
Subject: [PATCH 18/26] Update tracs to 1.0.1 (#51045)

---
 recipes/tracs/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/tracs/meta.yaml b/recipes/tracs/meta.yaml
index 27dd65f6653b3..c0f21db61532b 100644
--- a/recipes/tracs/meta.yaml
+++ b/recipes/tracs/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.0.0" %} 
+{% set version = "1.0.1" %} 
 {% set name = "tracs" %}
 
 package:
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://github.com/gtonkinhill/{{ name|lower }}/archive/v{{ version }}.tar.gz
-  sha256: 8950cf46bf53160b03c639cf9c1aaca43e506ac60b081d3ba7ee0a3b61c800f9
+  sha256: ea54a443c2a1a2bda7bb4dc9b79f79ffe5bfffc340ef8e6cc61f1df249ba4e5c
 
 build:
   number: 0
@@ -61,4 +61,4 @@ about:
   license_family: MIT
   license_file: LICENSE
   summary: 'Tracs - Fast pairwise transmission inference from single genome and/or metagenomic data'
-  doc_url: https://github.com/gtonkinhill/tracs/tree/main/docs
\ No newline at end of file
+  doc_url: https://github.com/gtonkinhill/tracs/tree/main/docs

From 57e8031a3026949542404f89b1923ba75e044145 Mon Sep 17 00:00:00 2001
From: Joon Klaps <joon.klaps@kuleuven.be>
Date: Mon, 30 Sep 2024 15:39:31 +0200
Subject: [PATCH 19/26] Add SpreadGLtools (#50627)

* init spreadGL

* succesfull build

* add name & pin versions

* change name to tools

* rename recipe spreadgl to spreadgltools

* adding gdal dependency

* add release url & include suggestions

* add dependency setuptools & fix typos

* fix lint & include coderabbitai suggestions

* removing unused cython dependency
---
 recipes/spreadgltools/meta.yaml | 60 +++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 recipes/spreadgltools/meta.yaml

diff --git a/recipes/spreadgltools/meta.yaml b/recipes/spreadgltools/meta.yaml
new file mode 100644
index 0000000000000..0cb09eeb3e772
--- /dev/null
+++ b/recipes/spreadgltools/meta.yaml
@@ -0,0 +1,60 @@
+{% set name ="SpreadGLtools" %}
+{% set version ="1.1.0" %}
+{% set sha256 ="de9319eb0cab7dcf042671c77fd473a7a03a8384ce7d476f10f89a8a100cbeec" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/GuyBaele/SpreadGL/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  noarch: python
+  script_env:
+    - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }}
+  script: |
+    cd scripts
+    {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  run_exports:
+    - {{ pin_subpackage(name|lower, max_pin="x") }}
+
+requirements:
+  host:
+    - python >=3.11
+    - pip
+  run:
+    - python >=3.11
+    - setuptools >=67.4.0
+    - numpy >=1.23.2
+    - pandas >=2.2.0
+    - geojson >=3.0.1
+    - pyproj >=3.4.1
+    - dendropy >=4.5.2
+    - geopandas >=0.12.2
+    - rasterio >=1.3.6
+    - rioxarray >=0.14.0
+    - bottleneck >=1.3.7
+    - gdal >=3.3.0
+
+test:
+  commands:
+    - spread --help
+    - rates --help
+    - regions --help
+    - raster --help
+    - reprojection --help
+    - trimming --help
+
+about:
+  home: https://github.com/GuyBaele/SpreadGL
+  license: MIT
+  summary: 'Visualising pathogen dispersal in a high-performance browser application'
+  license_family: MIT
+  doc_url: https://github.com/GuyBaele/SpreadGL
+
+extra:
+  identifiers:
+    - doi:10.1101/2024.06.04.24308447

From 37e8a567b74359317cc394d4a9993e0a82ee1fec Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 11:24:32 -0400
Subject: [PATCH 20/26] Update pytximport to 0.9.0 (#51049)

---
 recipes/pytximport/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/pytximport/meta.yaml b/recipes/pytximport/meta.yaml
index d7245d020c367..c27f43344082a 100644
--- a/recipes/pytximport/meta.yaml
+++ b/recipes/pytximport/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pytximport" %}
-{% set version = "0.8.0" %}
+{% set version = "0.9.0" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pytximport-{{ version }}.tar.gz
-  sha256: 18bdf4fbcd78092bba18f6941f5640a937b4f0230c30c2e8fca38ce207b3840b
+  sha256: f311705a71faa095d7e65de63235df55c805fbab4fbea10010fdae11014b3c95
 
 build:
   noarch: python

From 58dfab8c4c623ddf97f52c5d6fd31b8ab1a06fce Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 12:09:47 -0400
Subject: [PATCH 21/26] Update pybiolib to 1.2.185 (#51053)

---
 recipes/pybiolib/meta.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/recipes/pybiolib/meta.yaml b/recipes/pybiolib/meta.yaml
index ea22be4adc294..5b42a9cd463cf 100644
--- a/recipes/pybiolib/meta.yaml
+++ b/recipes/pybiolib/meta.yaml
@@ -1,5 +1,5 @@
 {% set name = "pybiolib" %}
-{% set version = "1.2.181" %}
+{% set version = "1.2.185" %}
 
 package:
   name: {{ name|lower }}
@@ -7,7 +7,7 @@ package:
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/pybiolib-{{ version }}.tar.gz
-  sha256: 6025ec0898d20ea83593144619b1c94b5f99b46955205a74537b97270924ce7f
+  sha256: 9525f0548dd11df88b33845ecf51d17ee9c2c5675a0723ebf5c25c586c58e598
 
 build:
   number: 0

From 6bedbb57390d60ab0648dd14872387c04677a9fa Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 12:09:57 -0400
Subject: [PATCH 22/26] Update cpstools to 2.0.0 (#51031)

* Update cpstools to 2.0.0

* add tqdm

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/cpstools/meta.yaml | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/recipes/cpstools/meta.yaml b/recipes/cpstools/meta.yaml
index f8dbea9224cbb..e9c88674e0521 100644
--- a/recipes/cpstools/meta.yaml
+++ b/recipes/cpstools/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "cpstools" %}
-{% set version = "1.0.13" %}
-{% set sha256 = "767f5739416f290726ed459bf82969b453ffd2c04aa9171e5dc7c842a8d6b81e" %}
+{% set version = "2.0.0" %}
+{% set sha256 = "1c2c729d4979402d9f7835dea70e47c77d2e2ef6b1e822cfd1e6e008f3b98ba1" %}
 
 package:
   name: {{ name|lower }}
@@ -21,13 +21,14 @@ build:
 
 requirements:
   host:
-    - python >=3.10
+    - python >=3.9
     - poetry-core
     - pip
   run:
-    - python >=3.10.0
+    - python >=3.9
     - biopython >=1.84.0
     - numpy >=1.26.4
+    - tqdm >=4.66.5
  
 test:
   imports:

From d8e872ace0811ce0c021003ae0853f50628c1523 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 12:10:23 -0400
Subject: [PATCH 23/26] Update bioconda-utils to 3.3.2 (#51044)

* Update bioconda-utils to 3.3.2

* pin python to <3.12

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/bioconda-utils/meta.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml
index 49d272da820fb..c8a92fc0b1c12 100644
--- a/recipes/bioconda-utils/meta.yaml
+++ b/recipes/bioconda-utils/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "bioconda-utils" %}
-{% set version = "3.3.1" %}
-{% set sha256 = "db6b99456a334b958ba61fcfc6e717e5f22848342f99fecb1f6f2b0113165054" %}
+{% set version = "3.3.2" %}
+{% set sha256 = "6c6dcac689a2fb0f8142546aa9021bfd620fe484e724e4844a2d2e55c337747c" %}
 
 package:
   name: {{ name }}
@@ -21,7 +21,7 @@ build:
 
 requirements:
   host:
-    - python
+    - python <3.12
     - pip
   run:
     - conda-forge-pinning 2024.06.01.05.54.15

From 3bb30cf0fe156b01999ffeb0ef8747539b329f3b Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 12:43:58 -0400
Subject: [PATCH 24/26] Update catfasta2phyml to 1.2.1 (#51052)

* Update catfasta2phyml to 1.2.1

* add run_exports

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/catfasta2phyml/meta.yaml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/recipes/catfasta2phyml/meta.yaml b/recipes/catfasta2phyml/meta.yaml
index 0127661fa44c0..44d06ac51bcaf 100644
--- a/recipes/catfasta2phyml/meta.yaml
+++ b/recipes/catfasta2phyml/meta.yaml
@@ -1,14 +1,16 @@
 package:
   name: catfasta2phyml
-  version: "1.2.0"
+  version: "1.2.1"
 
 source:
-  url: https://github.com/nylander/catfasta2phyml/archive/refs/tags/v.1.2.0.tar.gz
-  sha256: f4ea5aef5aa21d15d84436262f06b79a004b7017ab7a433019fe903aec995fdb
+  url: https://github.com/nylander/catfasta2phyml/archive/refs/tags/v1.2.1.tar.gz
+  sha256: 2647985192b05df49e10bfce64d6843fe7916b0395199dfd2ac4f80910c5a91f
 
 build:
   number: 0
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage('catfasta2phyml', max_pin="x") }}
 
 requirements:
   run:

From 4990d0b1bc93adfbba62bc59008e55b9398f495e Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 15:26:46 -0400
Subject: [PATCH 25/26] Update yahs to 1.2.2 (#51050)

* Update yahs to 1.2.2

* edit patch

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
Co-authored-by: Joshua Zhuang <71105179+mencian@users.noreply.github.com>
---
 recipes/yahs/Makefile.patch | 6 +++---
 recipes/yahs/meta.yaml      | 4 ++--
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/recipes/yahs/Makefile.patch b/recipes/yahs/Makefile.patch
index 347d4e9d7231d..263e6bffe6e59 100644
--- a/recipes/yahs/Makefile.patch
+++ b/recipes/yahs/Makefile.patch
@@ -1,10 +1,10 @@
 diff --git a/Makefile b/Makefile
-index 2174509..f7b8646 100644
+index 1cb880c..1c2283f 100644
 --- a/Makefile
 +++ b/Makefile
 @@ -1,4 +1,4 @@
--CFLAGS=		-g -O0 -Wall -fno-strict-aliasing
-+CFLAGS += -g -O0 -Wall -fno-strict-aliasing
+-CFLAGS=		-O3 -Wall -fno-strict-aliasing
++CFLAGS +=		-O3 -Wall -fno-strict-aliasing
  CPPFLAGS=
  INCLUDES=
  OBJS=
diff --git a/recipes/yahs/meta.yaml b/recipes/yahs/meta.yaml
index 47ca09ece7c7e..b4cc5e55f410f 100644
--- a/recipes/yahs/meta.yaml
+++ b/recipes/yahs/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.2.1" %}
+{% set version = "1.2.2" %}
 
 package:
   name: yahs
@@ -6,7 +6,7 @@ package:
 
 source:
   url: https://github.com/c-zhou/yahs/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 0e18c393424573323deecc4b71d1bf4620b74fc942cd0c8d056f57870bdd24c0
+  sha256: 9ee37f72ee9f62015fe92029d0fa97eec90963ddf15a2f4b760b45ee2e0014aa
   patches:
     - Makefile.patch
 

From 82c0af127517da733c6a1b4989d7f167b291afe5 Mon Sep 17 00:00:00 2001
From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com>
Date: Mon, 30 Sep 2024 17:09:14 -0400
Subject: [PATCH 26/26] Update sizemeup to 1.1.0 (#51055)

* Update sizemeup to 1.1.0

* Update test

---------

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
---
 recipes/sizemeup/meta.yaml | 97 +++++++++++++++++++-------------------
 1 file changed, 49 insertions(+), 48 deletions(-)

diff --git a/recipes/sizemeup/meta.yaml b/recipes/sizemeup/meta.yaml
index 990ed7e6a9e3d..904ca91666424 100644
--- a/recipes/sizemeup/meta.yaml
+++ b/recipes/sizemeup/meta.yaml
@@ -1,48 +1,49 @@
-{% set name = "sizemeup" %}
-{% set version = "1.0.2" %}
-
-package:
-  name: {{ name|lower }}
-  version: {{ version }}
-
-source:
-  url: https://github.com/rpetit3/sizemeup/archive/v{{ version }}.tar.gz
-  sha256: 0290d945909e20ccd417e4a874c22e14f5904695586974a98424dd9890bc9550
-
-build:
-  number: 0
-  noarch: generic
-  run_exports:
-    - {{ pin_subpackage(name, max_pin='x.x') }}
-
-requirements:
-  host:
-    - python >=3.7
-    - poetry
-    - pip
-  run:
-    - python >=3.7
-    - requests
-    - rich-click >=1.6.0
-
-test:
-  imports:
-    - sizemeup
-  commands:
-    - pip check
-    - sizemeup --version
-    - sizemeup --help
-    - sizemeup --species "Staphylococcus aureus"
-    - sizemeup-build --help
-  requires:
-    - pip
-
-about:
-  home: https://github.com/rpetit3/sizemeup
-  summary: A simple tool to determine the genome size of an organism
-  license: MIT
-  license_file: LICENSE
-
-extra:
-  recipe-maintainers:
-    - rpetit3
+{% set name = "sizemeup" %}
+{% set version = "1.1.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/rpetit3/sizemeup/archive/v{{ version }}.tar.gz
+  sha256: 3941e0b6affa2ba69c6ee01875d38ed8a94b864fbf51c4971a811d5483a61b8c
+
+build:
+  number: 0
+  noarch: generic
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  host:
+    - python >=3.7
+    - poetry
+    - pip
+  run:
+    - python >=3.7
+    - requests
+    - rich-click >=1.6.0
+
+test:
+  imports:
+    - sizemeup
+  commands:
+    - pip check
+    - sizemeup --version
+    - sizemeup --help
+    - sizemeup --query "Staphylococcus aureus"
+    - sizemeup -q 1280
+    - sizemeup-build --help
+  requires:
+    - pip
+
+about:
+  home: https://github.com/rpetit3/sizemeup
+  summary: A simple tool to determine the genome size of an organism
+  license: MIT
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - rpetit3