Merge branch 'master' into gbintk

bioconda · Sep 27, 2024 · 0967a96 · 0967a96
2 parents 62d3b9d + a59edd4
commit 0967a96
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diff --git a/recipes/architeuthis/meta.yaml b/recipes/architeuthis/meta.yaml
@@ -1,16 +1,16 @@
 {% set name = "architeuthis" %}
-{% set version = "0.3.0" %}
+{% set version = "0.3.1" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
   url: https://github.com/cdiener/{{ name }}/archive/{{ version }}.tar.gz
-  sha256: 63aba50c66188202debc822d0ded57d2398f5e4e9d8535f83a2c5e982bb4999f
+  sha256: 11b0e09785f23e479f3de55e12dfbe788c938a497a64c7293d8c4ce41d57ef2b
 
 build:
-  number: 1
+  number: 0
   script:
     - go build -v -ldflags "-w -s -X 'main.version={{ version }}'" -o $PREFIX/bin/architeuthis
   run_exports:

diff --git a/recipes/biobb_structure_checking/meta.yaml b/recipes/biobb_structure_checking/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "biobb_structure_checking" %}
-{% set version = "3.13.4" %}
+{% set version = "3.13.5" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
-  sha256: d819819d13c7ad219411b70b043555dcd65d5535f696a1121db562646931f445
+  sha256: 4ba074da556a7aecac215f2020a04274c05f155413ed467177b9c9f31a53d4d0
 
 build:
   number: 0

diff --git a/recipes/dxpy/meta.yaml b/recipes/dxpy/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "dxpy" %}
-{% set version = "0.382.0" %}
+{% set version = "0.383.1" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: c8427fdc2d293622e2fa250afe6e51fc85a21c5abed697be863eb7a644c502e7
+  sha256: 377af4014a5f27efd6fe9478d0fa9c30ced245947fbd2e2e5713c8a37db598b0
 
 build:
   number: 0

diff --git a/recipes/falco/build.sh b/recipes/falco/build.sh
@@ -7,16 +7,22 @@ export M4="$BUILD_PREFIX/bin/m4"
 # add Configuration and example files to opt
 falco=$PREFIX/opt/falco
 mkdir -p $falco
-cp -r ./* $falco
+cp -rf ./* $falco
 
 #to fix problems with htslib
 export C_INCLUDE_PATH=$C_INCLUDE_PATH:${PREFIX}/include
 export CPLUS_INCLUDE_PATH=$CPLUS_INCLUDE_PATH:${PREFIX}/include
 export LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib
 export LD_LIBRARY_PATH=$LIBRARY_PATH:${PREFIX}/lib
 
+export INCLUDES="-I{PREFIX}/include"
+export LIBPATH="-L${PREFIX}/lib"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+export CXXFLAGS="${CXXFLAGS} -O3 -I{PREFIX}/include"
+
 cd $falco
-./configure --prefix=$falco --enable-hts
+autoreconf -if
+./configure --prefix=$falco --enable-hts CXX="${CXX}" CXXFLAGS="${CXXFLAGS}"
 make -j ${CPU_COUNT}
 make install
 for i in $(ls -1 | grep -v Configuration | grep -v bin);

diff --git a/recipes/falco/meta.yaml b/recipes/falco/meta.yaml
@@ -1,40 +1,41 @@
-{% set version = "1.2.3" %}
+{% set version = "1.2.4" %}
 
 package:
   name: falco
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   run_exports:
     # falco is currently not intended to be stable between minor versions (x.x).
     - {{ pin_subpackage('falco', max_pin="x.x") }}
 
-
 source:
   url: https://github.com/smithlabcode/falco/releases/download/v{{ version }}/falco-{{ version }}.tar.gz
-  sha256: b2d4da736efecfa669ad555fbb69862bc7fb57dcf32efcb6c151c47f98b32b8a
+  sha256: 116c257fbf87bf99083d8e539a51ce74bc5a8d141f99a437a0c23e9d1379096a
 
 requirements:
   build:
     - make
     - {{ compiler('cxx') }}
     - autoconf
     - automake
+    - libtool
   host:
     - zlib
     - htslib
   run:
-    - zlib
     - htslib
 
 about:
-  home: https://github.com/smithlabcode/falco
+  home: 'https://github.com/smithlabcode/falco'
   license: GPL-3.0-only
+  license_family: GPL3
   license_file: LICENSE
   summary: |
     falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads.
-  doc_url: 'https://falco.readthedocs.io/'
+  doc_url: 'https://falco.readthedocs.io'
+  dev_url: 'https://github.com/smithlabcode/falco'
 
 test:
   commands:

diff --git a/recipes/genomedata/meta.yaml b/recipes/genomedata/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "genomedata" %}
-{% set version = "1.7.2" %}
-{% set sha256 = "588efabd6a163af059e945aa6c638b9e9129ab46f27c4a35baafdbfb5f7edbbd" %}
+{% set version = "1.7.3" %}
+{% set sha256 = "308a2110ec14659f4a9e40d1515e5d9c95ebf808923f0cfbbe5cff4e7a8cce3c" %}
 
 package:
   name: {{ name|lower }}
@@ -12,7 +12,7 @@ source:
 
 build:
   skip: True  # [osx or py < 39]
-  number: 2
+  number: 0
   entry_points:
     - genomedata-close-data = genomedata._close_data:main
     - genomedata-erase-data = genomedata._erase_data:main

diff --git a/recipes/gget/meta.yaml b/recipes/gget/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "gget" %}
-{% set version = "0.28.6" %}
-{% set sha256 = "4cbc60e967a30d79878525cbae64871bf1f7c764427a689a7f55e52720b01f82" %}
+{% set version = "0.29.0" %}
+{% set sha256 = "5af54af941477bead501d66a0509a8bcf672ba637ef0750bb3faef79959512e3" %}
 
 package:
   name: "{{ name|lower }}"
@@ -21,26 +21,26 @@ build:
 
 requirements:
   host:
-    - python >=3.6
+    - python >=3.7
     - pip
     - bs4
     - requests >=2.22.0
     - pandas >=1.0.0
     - ipython
-    - mysql-connector-python >=8.0.5,<=8.0.29
+    - mysql-connector-python >=8.0.32
     - matplotlib-base
     - tqdm
     - ipywidgets
     - lxml
     - numpy >=1.17.2
   run:
-    - python >=3.6
+    - python >=3.7
     - numpy >=1.17.2
     - pandas >=1.0.0
     - requests >=2.22.0
     - ipython
     - matplotlib-base
-    - mysql-connector-python >=8.0.5,<=8.0.29
+    - mysql-connector-python >=8.0.32
     - bs4 >=4.10.0
     - ipywidgets
     - tqdm
@@ -60,10 +60,10 @@ test:
 
 about:
   home: "https://github.com/pachterlab/gget"
-  license: BSD-2-Clause
+  license: "BSD-2-Clause"
   license_family: BSD
   license_file: LICENSE
-  summary: "gget enables efficient querying of genomic databases"
+  summary: "gget enables efficient querying of genomic databases."
   description: |
     gget enables efficient querying of genomic databases, such as Ensembl, UniProt, 
     NCBI, directly into a Python or terminal programming environment. It was 
@@ -75,3 +75,5 @@ extra:
   recipe-maintainers:
     - nh13
     - lauraluebbert
+  identifiers:
+    - doi:10.1093/bioinformatics/btac836
diff --git a/recipes/graphbin2/meta.yaml b/recipes/graphbin2/meta.yaml
@@ -1,13 +1,13 @@
 {% set name = "GraphBin2" %}
-{% set version = "1.3.2" %}
+{% set version = "1.3.3" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://github.com/metagentools/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz"
-  sha256: 5cb611d539ac2608cf262ea5db39e4d81bc7c9c1a53ea2f5a47fb5d8abcb848a
+  sha256: 03ab89dbb6d26c9b414ff808598c295cf22fd3af22816a5c9fada94104a79686
 
 build:
   number: 0

diff --git a/recipes/hopla/meta.yaml b/recipes/hopla/meta.yaml
@@ -10,8 +10,10 @@ source:
   sha256: {{ hash }}
 
 build:
-  number: 0
+  number: 1
   noarch: generic
+  run_exports:
+    - {{ pin_subpackage("hopla", max_pin="x") }}
 
 requirements:
   run:
@@ -26,7 +28,7 @@ requirements:
     - bioconductor-genomicranges >=1.42.0
     - bioconductor-dnacopy >=1.64.0
     - merlin 1.1.2.*  # [not osx]
-    - pandoc >=2.*
+    - pandoc >=3.1.5
 
 test:
   commands:

diff --git a/recipes/kmertools/meta.yaml b/recipes/kmertools/meta.yaml
@@ -1,6 +1,6 @@
-{% set version = "0.1.3" %}
+{% set version = "0.1.4" %}
 {% set name = "kmertools" %}
-{% set sha256 = "02892ce148db4043bede10267f390c9fea14d49f65b43e1f05092153939bd5e0" %}
+{% set sha256 = "457ffdbe2cc34b9faf63d06124d6d68ffc9b8c83825fc800d171899dc3a8b0d9" %}
 
 package:
   name: {{ name }}

diff --git a/recipes/metabolabpy/meta.yaml b/recipes/metabolabpy/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "metabolabpy" %}
-{% set version = "0.9.47" %}
-{% set sha256 = "9598c8df848403b31f98c926e053788ce9aed8d3e69749331fcb8393d460416c" %}
+{% set version = "0.9.50" %}
+{% set sha256 = "9fe9e080e72a7ed26d2ddaf32730a2b5a9edf752bef3aeb4b242b49b17813686" %}
 
 package:
   name: {{ name|lower }}

diff --git a/recipes/metacoag/meta.yaml b/recipes/metacoag/meta.yaml
@@ -1,17 +1,16 @@
 {% set name = "MetaCoAG" %}
-{% set version = "1.2.1" %}
+{% set version = "1.2.2" %}
 
 package:
   name: "{{ name|lower }}"
   version: "{{ version }}"
 
 source:
   url: "https://github.com/metagentools/{{ name }}/archive/v{{ version }}.tar.gz"
-  sha256: 5962a92e49842f55db50b7a7bede8dc33b9508a08d395a796b3f4fa78fed70b9
+  sha256: 1a8d91cb02fdad9ba15c636eeaf167e34f118bc4d12f57366e107ebf160781c7
 
 build:
   number: 0
-  noarch: python
   entry_points:
     - metacoag = metacoag.cli:main
     - combine_cov = metacoag.metacoag_utils.support.combine_cov:main
@@ -56,6 +55,8 @@ about:
   dev_url: "https://github.com/metagentools/MetaCoAG"
 
 extra:
+  skip-lints:
+    - should_be_noarch_generic
   recipe-maintainers:
     - Vini2
   identifiers:

diff --git a/recipes/moni/build.sh b/recipes/moni/build.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+set -xe
+
+export CPATH=$PREFIX/include:$CPATH
+export LIBRARY_PATH=$PREFIX/lib:$LIBRARY_PATH
+export LD_LIBRARY_PATH=$PREFIX/lib:$LD_LIBRARY_PATH
+
+mkdir build
+cd build
+cmake -DCMAKE_INSTALL_PREFIX=$PREFIX \
+      -DCMAKE_PREFIX_PATH=$PREFIX \
+      -DCMAKE_INCLUDE_PATH=$PREFIX/include \
+      -DCMAKE_LIBRARY_PATH=$PREFIX/lib \
+      -DZLIB_ROOT=$PREFIX \
+      ..
+make -j ${CPU_COUNT} VERBOSE=1
+make install
diff --git a/recipes/moni/conda_build_config.yaml b/recipes/moni/conda_build_config.yaml
@@ -0,0 +1,5 @@
+c_compiler_version:
+  - 9.3.0 # [linux]
+
+cxx_compiler_version:
+  - 9.3.0 # [linux]
diff --git a/recipes/moni/meta.yaml b/recipes/moni/meta.yaml
@@ -0,0 +1,54 @@
+{% set name = "moni" %}
+{% set version = "0.2.2" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/maxrossi91/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 638cd590e0c91218a9c7c0bf5aac6289d445a5a1b3ad91aa0cf62d7ff57ce0ce 
+
+build:
+  skip: True # [osx]
+  number: 0
+  run_exports:
+      - {{ pin_subpackage(name, max_pin='x.x') }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+    - make
+    - git
+  host:
+    - zlib
+    - python
+  run:
+    - zlib
+    - python
+
+test:
+  commands:
+    - moni -h
+    - moni build -h
+    - moni ms -h
+    - moni mems -h
+    - moni extend -h
+
+about:
+  home: https://github.com/maxrossi91/moni
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: 'A Pangenomics Index for Finding MEMs'
+  description: |
+    MONI (Multi) is a Pangenomics Index for Finding Maximal Exact Matches (MEMs).
+    It uses the prefix-free parsing of the text to build the Burrows-Wheeler Transform (BWT) 
+    of the reference genomes, the suffix array (SA) samples at the beginning and at the end 
+    of each run of the BWT, and the threshold positions.
+
+extra:
+  recipe-maintainers:
+    - AndreaGuarracino
+    - maxrossi91