Merge branch 'master' into gzrt

bioconda · Nov 3, 2024 · 0e40b4d · 0e40b4d
2 parents 4fcd404 + f4f4918
commit 0e40b4d
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diff --git a/ntstat/build.sh b/ntstat/build.sh
@@ -0,0 +1,4 @@
+#!/usr/bin/env bash
+
+meson setup --buildtype release --prefix=$PREFIX build
+meson install -C build
diff --git a/ntstat/meta.yaml b/ntstat/meta.yaml
@@ -0,0 +1,48 @@
+{% set version = "1.0.0" %}
+
+package:
+  name: ntstat
+  version: {{ version }}
+
+source:
+  url: https://github.com/bcgsc/ntStat/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 262dc58ab6f781a6816a5d4fc129659c7fa2c3364871320eafb45bfa822fab6a
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage('ntstat', max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - meson
+    - meson-python
+    - cmake
+  host:
+    - python
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
+    - btllib >=1.7.2
+    - cpp-argparse
+    - cpp-tabulate
+    - indicators
+    - pybind11
+  run:
+    - python
+    - ntcard
+    - matplotlib
+    - numpy
+    - scipy
+    - tabulate
+
+test:
+  commands:
+    - ntstat --version
+    - ntstat count --help
+
+about:
+  home: https://github.com/bcgsc/ntStat
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+  summary: 'a toolkit for statistical analysis of k-mer frequency and depth'
diff --git a/recipes/amplici/build.sh b/recipes/amplici/build.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+
+if [[ `uname` == "Darwin" ]]; then
+    export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
+else
+    export CONFIG_ARGS=""
+fi
+
+cd src || exit 1
+cmake -S . -B build -DCMAKE_BUILD_TYPE=Release \
+    -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
+    -DCMAKE_C_COMPILER="${CC}" \
+    -DCMAKE_C_FLAGS="${CFLAGS}" \
+    "${CONFIG_ARGS}"
+cmake --build build --target install -j "${CPU_COUNT}" -v
diff --git a/recipes/amplici/meta.yaml b/recipes/amplici/meta.yaml
@@ -0,0 +1,46 @@
+{% set version = "2.2" %}
+
+package:
+  name: amplici
+  version: {{ version }}
+
+source:
+  url: https://github.com/DormanLab/AmpliCI/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 273362b5449ec29ff411d4c1aa5f89b1ec1eb361c8a9b69a4d89f4409fbdb70e
+
+build:
+  number: 0
+  run_exports:
+    - {{ pin_subpackage("amplici", max_pin="x") }}
+
+requirements:
+  build:
+    - cmake
+    - make
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - {{ compiler('fortran') }}
+  host:
+    - zlib
+
+about:
+  home: https://github.com/DormanLab/AmpliCI
+  license: BSD 3-Clause
+  license_family: BSD
+  license_file: LICENSE  
+  summary: "AmpliCI: Cluster amplicon sequences in a fastq file with or without UMIs."
+  dev_url: https://github.com/DormanLab/AmpliCI
+
+test:
+  commands:
+    - run_AmpliCI -h
+
+extra:
+  additional-platforms:
+    - linux-aarch64
+    - osx-arm64
+  recipe-maintainers:
+    - xiyupeng
+  identifiers:
+    - biotools:amplici
+    - doi:10.1093/bioinformatics/btaa648
diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "1.34.0" %}
+{% set version = "1.38.0" %}
 {% set name = "ProtGenerics" %}
-{% set bioc = "3.18" %}
+{% set bioc = "3.20" %}
 
 package:
   name: 'bioconductor-{{ name|lower }}'
@@ -11,7 +11,7 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
     - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: 5d55c00588169aa089bb457e2d94669a
+  md5: 7e7211a9fa758ca6f1b701c86e892895
 build:
   number: 0
   rpaths:

diff --git a/recipes/csvtk/meta.yaml b/recipes/csvtk/meta.yaml
@@ -1,24 +1,24 @@
-{% set version = "0.30.0" %}
+{% set version = "0.31.0" %}
 # This package should be migrated to conda-forge due to general utility
 # In that case it needs to be built from source
 package:
   name: csvtk
   version: {{ version }}
 
 build:
-  number: 2
+  number: 0
   run_exports:
     - {{ pin_subpackage('csvtk', max_pin='x.x') }}
 
 source:
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_amd64.tar.gz # [osx and x86_64]
-    md5: c415255e265ba0cd547806fdbda05652 # [osx and x86_64]
+    md5: 5a23d000a1fc068360e1aeb439f3ae25 # [osx and x86_64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_darwin_arm64.tar.gz # [arm64]
-    md5: dd8a84c301d378ab7ff28c85d37fbefa # [arm64]
+    md5: 6aa24ce286910e83d95d28a21905f1d8 # [arm64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_amd64.tar.gz # [linux and x86_64]
-    md5: 8f5877d4fbea89609d64bd2679956476 # [linux and x86_64]
+    md5: 09bc8c3288f028239c94d4c935ac7a6f # [linux and x86_64]
   - url: https://github.com/shenwei356/csvtk/releases/download/v{{ version }}/csvtk_linux_arm64.tar.gz # [aarch64]
-    md5: 2a6dd840291d23971ff538eaf3de00ec # [aarch64]
+    md5: f7a5b8839459d7d55685056331670eec # [aarch64]
 
 test:
   commands:

diff --git a/recipes/fgbio-minimal/meta.yaml b/recipes/fgbio-minimal/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "2.3.0" %}
+{% set version = "2.4.0" %}
 
 package:
   name: fgbio-minimal
   version: {{ version }}
 
 source:
   url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar
-  sha256: a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69
+  sha256: c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937
 
 build:
   noarch: generic

diff --git a/recipes/fgbio/meta.yaml b/recipes/fgbio/meta.yaml
@@ -1,12 +1,12 @@
-{% set version = "2.3.0" %}
+{% set version = "2.4.0" %}
 
 package:
   name: fgbio
   version: {{ version }}
 
 source:
   url: https://github.com/fulcrumgenomics/fgbio/releases/download/{{ version }}/fgbio-{{ version }}.jar
-  sha256: a0748b52a92403d88e7cf799368c313a05f89c5e3da04f7f8829593a603b7c69
+  sha256: c8f4df9d6f4f34998e9f5d6f6533ca4fc87170247f7156d7d9705e25daee2937
 
 build:
   noarch: generic

diff --git a/recipes/fgsv/meta.yaml b/recipes/fgsv/meta.yaml
@@ -1,5 +1,5 @@
-{% set version="0.2.0" %}
-{% set sha256="c2f9536a677e7e99f251cada1338f611cea40477deca144f0c6928505755eb37" %}
+{% set version="0.2.1" %}
+{% set sha256="e3f15c7f1a97c009be65663405194faedf473c2636a3c3d742f463030caba860" %}
 
 
 package:

diff --git a/recipes/goldrush/meta.yaml b/recipes/goldrush/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "goldrush" %}
-{% set version = "1.2.0" %}
+{% set version = "1.2.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/bcgsc/goldrush/releases/download/{{ version }}/{{ name|lower }}-{{ version }}.tar.gz
-  sha256: 3f70860ed92b9313dbab16efed65ea7bc6080d78b4e18afc8cb910e086a7f0f7
+  sha256: 0b8b91b0477510d341af1736539416f30f70f67af9bd84161ea51c4c4a0fcc39
 
 build:
   skip: true  # [py < 38 or win or py > 39]

diff --git a/recipes/gsmap/meta.yaml b/recipes/gsmap/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "gsmap" %}
-{% set version = "1.71.1" %}
+{% set version = "1.71.2" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/gsMap/{{ name }}-{{ version }}.tar.gz"
-  sha256: f81debacf46d3e26614411d938a27345fcb42999a8ef2b740d134e910c2d0bcd
+  sha256: d058fb9c1e346b40cf3e6a1cf27fc6458acf3cdb29eb7d4dd74cb119ab0f88a9
 
 build:
   noarch: python

diff --git a/recipes/lotus2/build.sh b/recipes/lotus2/build.sh
@@ -1,10 +1,10 @@
 #!/bin/sh
 SHARE_DIR=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM
 
-rm -rf bin/installs/ bin/LCA bin/rtk bin/sdm bin/vsearch configs/sdm_src/
+rm -rf bin/installs/ bin/lambda3* bin/LCA bin/rtk bin/sdm bin/vsearch
 # Configure LotuS2
 cp configs/LotuS.cfg.def lOTUs.cfg
-for binary in blastn clustalo lambda3 LCA mafft minimap2 rtk sdm swarm vsearch; do
+for binary in blastn clustalo lambda3 LCA mafft minimap2 rtk sdm swarm usearch vsearch; do
     sed -i.bak -e "s|^$binary[[:space:]].*|$binary $PREFIX/bin/$binary|" lOTUs.cfg
 done
 for binary in cd-hit fasttree hmmsearch iqtree itsx makeBlastDB RDPjar; do

diff --git a/recipes/lotus2/meta.yaml b/recipes/lotus2/meta.yaml
@@ -11,7 +11,7 @@ source:
   sha256: {{ sha256 }}
 
 build:
-  number: 0
+  number: 1
   noarch: generic
   run_exports:
     - {{ pin_subpackage(name, max_pin='x') }}

diff --git a/recipes/msa4u/meta.yaml b/recipes/msa4u/meta.yaml
@@ -0,0 +1,40 @@
+{% set name = "msa4u" %}
+{% set version = "0.4.0" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/msa4u-{{ version }}.tar.gz
+  sha256: 0471f334bbc1fbb8ea6c0974c39f9aed59030b32d3d790caf814c8f53c393c17
+
+build:
+  run_exports:    
+    - {{ pin_subpackage("msa4u", max_pin="x.x") }}
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  noarch: python
+
+requirements:
+  host:
+    - python
+    - pip
+  run:
+    - python
+    - biopython
+    - pandas
+    - reportlab
+    - configs
+
+test:
+  imports:
+    - msa4u
+  commands:
+    - msa4u --help
+
+about:
+  home: https://github.com/GCA-VH-lab/msa4u
+  summary: "A simple visualisation tool for Multiple Sequence Alignment."
+  license: WTFPL
+  license_file: LICENSE
diff --git a/recipes/muscle/build.sh b/recipes/muscle/build.sh
@@ -1,9 +1,18 @@
 #!/bin/bash
+set -e
 
-cd src/
-sed -i.bak -e 's/ -static//' Makefile
+mkdir -p ${PREFIX}/bin
+cd src || exit 1
+echo "0" > gitver.txt
 
-make CXX=$CXX
+cp ${RECIPE_DIR}/vcxproj_make.py .
+chmod +x vcxproj_make.py
+./vcxproj_make.py --openmp --cppcompiler ${CXX}
 
-mkdir -p "$PREFIX"/bin
-cp "$(uname)"/muscle "$PREFIX"/bin/muscle
+# Verify binary exists and is executable
+if [ ! -x ../bin/muscle ]; then
+    echo "Error: muscle binary not found"
+    exit 1
+fi
+
+cp ../bin/muscle ${PREFIX}/bin/muscle
diff --git a/recipes/muscle/meta.yaml b/recipes/muscle/meta.yaml
@@ -1,18 +1,18 @@
 {% set name = "muscle" %}
-{% set version = "5.1.0" %}
+{% set version = "5.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://github.com/rcedgar/muscle/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d
+  url: https://github.com/rcedgar/muscle/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 7aff1473241a36da94a88f37920a343fae91d2b6faae22e15c06591d1d0339b6
   patches:
     - support-linux-aarch64.patch
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
@@ -30,7 +30,7 @@ about:
   home: https://github.com/rcedgar/muscle
   license: GPL-3.0-only
   license_file: LICENSE
-  summary: "MUSCLE: multiple sequence alignment with high accuracy and high throughput"
+  summary: Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences
 
 extra:
   additional-platforms:

diff --git a/recipes/muscle/support-linux-aarch64.patch b/recipes/muscle/support-linux-aarch64.patch
@@ -1,10 +1,10 @@
-diff --git i/src/myutils.h w/src/myutils.h
-index 49d28ef..8e8167e 100644
---- i/src/myutils.h
-+++ w/src/myutils.h
-@@ -11,7 +11,7 @@
- #define TRACK_ALLOC		0
- #define ALLOC_TOTALS	0
+diff --git a/src/myutils.h b/src/myutils.h
+index a5d8a58..fbf6f9f 100644
+--- a/src/myutils.h
++++ b/src/myutils.h
+@@ -10,7 +10,7 @@
+ #include <cstddef>
+ #include "myalloc.h"
 
 -#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__)
 +#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__) || defined(__aarch64__)