Merge branch 'master' into bulk

recipes/assemblycomparator2/build.sh

@@ -1,20 +1,14 @@
-#!/usr/bin/env bash
+#!/bin/bash -euo
 
-
-# First we put the necessary files in into the conda prefix directory:
-mkdir -p ${PREFIX}/assemblycomparator2
-cp asscom2 snakefile config.yaml LICENSE ${PREFIX}/assemblycomparator2
-cp -r assets conda_definitions profiles report_subpipeline scripts tests ${PREFIX}/assemblycomparator2
-
-# This is the binary that we wish to be able to run.
 mkdir -p ${PREFIX}/bin
-ln -s ${PREFIX}/assemblycomparator2/asscom2 ${PREFIX}/bin/asscom2
 
+export PACKAGE_HOME="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}-${PKG_BUILDNUM}"
 
-# # I hope these variables are accessible when the user activates the environment that runs ac2.
-# ASSCOM2_BASE=$PREFIX
-# ASSCOM2_PROFILE=${ASSCOM2_BASE}/profiles/apptainer/local
-# ASSCOM2_DATABASES=${ASSCOM2_BASE}/databases # The user should override this in their .bashrc if they want to use a different dir.
+# First we put the necessary files in into the conda prefix/share directory:
+mkdir -p "${PACKAGE_HOME}"
+chmod 755 asscom2
+cp -f asscom2 workflow/Snakefile config/config.yaml "${PACKAGE_HOME}"
+cp -rf docs profile workflow/scripts tests "${PACKAGE_HOME}"
 
-# # I think it is better to use backslash-sentinel, because then the user can change the variables after having activated the PREFIX environment, and the changes will have effect
-# alias asscom2='snakemake --snakefile \${ASSCOM2_BASE}/snakefile --profile \${ASSCOM2_PROFILE} --configfile \${ASSCOM2_BASE}/config.yaml'
+# This is the binary that we wish to be able to run.
+ln -sf ${PACKAGE_HOME}/asscom2 ${PREFIX}/bin/asscom2

recipes/assemblycomparator2/meta.yaml

@@ -1,40 +1,41 @@
-{% set version = "2.6.2" %}
+{% set name = "assemblycomparator2" %}
+{% set version = "2.7.1" %}
+{% set sha256 = "20d02a94fef9565c21b93c108a5ff95797563a6ec40bd016a581de68ffccca60" %}
 
 package:
-  name: assemblycomparator2
+  name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/cmkobel/assemblycomparator2/archive/refs/tags/v{{ version }}.tar.gz
-  sha256: 52d1465c0da1955ee58848043309db81e551a87428e8b10fc55c02437addf6b8
-
+  sha256: {{ sha256 }}
 
 build:
   number: 0
+  noarch: generic
   run_exports:
-    - asscom2
-  skip: True # [osx]
+    - {{ pin_subpackage('assemblycomparator2', max_pin="x") }}
 
 requirements:
   run:
-    - snakemake =7.32.4
-    - mamba >=1.4.9 # Necessary for snakemake to install child environments during development.
-
+    - python >=3.11
+    - snakemake-minimal <8
+    - pulp <2.8
+    - mamba >=1.5.8  # Necessary for snakemake to install child environments during development.
 
 test:
   commands:
-    - touch dummy.fa; asscom2 --help
-
+    - "touch dummy.fa; asscom2 --help"
 
 about:
-  home: https://github.com/cmkobel/assemblycomparator2
+  home: "https://github.com/cmkobel/assemblycomparator2"
   summary: 'assemblycomparator2: Compare prokaryotic genomic assemblies'
-  license_family: GPL
-  license: GPL-3.0
+  license_family: GPL3
+  license: "GPL-3.0-or-later"
   license_file: LICENSE
+  dev_url: "https://github.com/cmkobel/assemblycomparator2"
+  doc_url: "https://assemblycomparator2.readthedocs.io/en/latest"
+
 extra:
-  skip-lints:
-    - should_be_noarch_generic
   recipe-maintainers:
     - cmkobel
-

recipes/bacpage/meta.yaml

@@ -1,26 +1,29 @@
-{% set version = "2023.11.10.1" %}
+{% set name = "bacpage" %}
+{% set version = "2024.03.08" %}
 
 package:
-  name: bacpage
+  name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/CholGen/bacpage/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 7a62278131407195a8f7555a92ed2d86ca7e63366bac6d280dac337e5f5218c5 
+  sha256: a0344f0e6c218a2e9a54a3d63eecc143c5d05ad3b0c4bf4379e34369b6ee53a7
 
 build:
   number: 0
   noarch: python
-  script: "{{ PYTHON }} -m pip install --no-deps --ignore-installed ."
+  script: "{{ PYTHON }} -m pip install --no-deps --no-build-isolation --no-cache-dir . -vvv"
+  entry_points:
+    - bacpage = bacpage.command:main
   run_exports:
-    - {{ pin_subpackage('bacpage') }}
+    - {{ pin_subpackage('bacpage', max_pin=None) }}
 
 requirements:
   host:
-    - python <3.12,>=3.9
+    - python >=3.9,<3.12
     - pip
   run:
-    - python <3.12,>=3.9
+    - python >=3.9,<3.12
     - bc
     - bcftools =1.17
     - bedtools
@@ -47,14 +50,16 @@ test:
   commands:
     - bacpage -h
     - bacpage version
-    - bacpage example "$(mktemp -d)"
+    - bacpage setup "$(mktemp -d)"
 
 about:
   home: https://github.com/CholGen/bacpage
   license: "GPL-3.0-or-later"
+  license_family: GPL3
   license_file: LICENSE
   summary: An easy-to-use pipeline for the assembly and analysis of bacterial genomes
-
+  doc_url: https://cholgen.github.io/sequencing-resources/bacpage-command.html
+  dev_url: https://github.com/CholGen/bacpage
 
 extra:
   recipe-maintainers:

recipes/batch_brb/meta.yaml

@@ -1,12 +1,12 @@
-{% set version = "1.1" %}
+{% set version = "1.1.1" %}
 
 package:
   name: batch_brb
   version: {{ version }}
 
 source:
   url: https://github.com/erin-r-butterfield/batch_brb/archive/v{{ version }}.tar.gz
-  sha256: 91f75948d965e5966facd887321bf3e673d10c7f071ee6c73823b38e4b454e80
+  sha256: cb31cb2b69b76728ccb76e507ae1b54df9c88d3cbcb45d3313ca31cbb2784db6
 
 build:
   number: 0

recipes/bioconda-utils/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "bioconda-utils" %}
-{% set version = "3.2.0" %}
-{% set sha256 = "28e27bd72968f71084c53dcdce2c7b5911043cec2dae72a766497c51d5e57ff1" %}
+{% set version = "3.3.0" %}
+{% set sha256 = "c21f3c75993b00793feb703be80d6c0f8bb34e04f3a4042e007941fe7f156406" %}
 
 package:
   name: {{ name }}
@@ -24,7 +24,7 @@ requirements:
     - python
     - pip
   run:
-    - conda-forge-pinning 2023.05.06.13.08.41
+    - conda-forge-pinning 2024.06.01.05.54.15
     - python 3.10.*
     - conda 24.5.*
     - conda-libmamba-solver 24.1.*

recipes/clair3-illumina/meta.yaml

@@ -1,13 +1,13 @@
 {% set name = "clair3-illumina" %}
-{% set version = "1.0.8" %}
+{% set version = "1.0.9" %}
 
 package:
   name: {{ name }}
   version: {{ version }}
 
 source:
   url: https://github.com/HKU-BAL/Clair3/archive/refs/tags/v{{ version }}.zip
-  sha256: cd56e3d4c6a1e7f68f5aed7494eec13618eb12764b2f5cb38fdcfe1dbd01ae53
+  sha256: 79a697046c649daeb1df85a9d65c1a40f61816c4f0497d218192ed557b5d79b1
 
 build:
   number: 0

recipes/clinker-py/meta.yaml

@@ -1,26 +1,29 @@
 {% set name = "clinker" %}
-{% set version = "0.0.28" %}
-
+{% set version = "0.0.29" %}
 
 package:
   name: {{ name }}-py
   version: "{{ version }}"
 
 source:
   url: https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz
-  sha256: 2198d5bdbef75d5cb3224449666c3cc79f3d79459ade694e1bcdf1bf62c4a007
+  sha256: cca735b27da29fc676517d5578c771d05dd2be4f00ea25221747088185bd860d
 
 build:
   number: 0
   noarch: python
-  script: {{ PYTHON }} -m pip install . --no-deps --ignore-installed -vv
+  script: {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
+  entry_points:
+    - clinker=clinker.main:main
+  run_exports:
+    - {{ pin_subpackage('clinker-py', max_pin="x.x") }}
 
 requirements:
   host:
     - pip
-    - python
+    - python >=3.6
   run:
-    - python
+    - python >=3.6
     - disjoint-set >=0.7.1
     - biopython >=1.78
     - numpy >=1.13.3
@@ -36,7 +39,10 @@ about:
   license: MIT
   license_family: MIT
   summary: "Gene cluster comparison figure generator"
+  dev_url: "https://github.com/gamcil/clinker"
+  doc_url: "https://github.com/gamcil/clinker/blob/master/README.md"
 
 extra:
   identifiers:
-    - doi:10.5281/zenodo.4326585
+    - doi:10.1093/bioinformatics/btab007
+    - biotools:clinker

recipes/cojac/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "cojac" %}
-{% set version = "0.9.1" %}
-{% set sha256 = "64b8f0eec1ccda1f0de2a5adbff68adf50e4f483210d97a8b85c65354317c1a9" %}
+{% set version = "0.9.2" %}
+{% set sha256 = "ffdfd2e9c65daaddcbdd9664dfdcea4a77bf5a0884f84cb77ae11c4d5156cc99" %}
 
 package:
   name: {{ name|lower }}
@@ -25,6 +25,7 @@ requirements:
     - python
     - pip
     - poetry-core >=1.0.8
+    - poetry-dynamic-versioning
   run:
     - python
     - pysam >=0.17

recipes/deeplc/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "DeepLC" %}
-{% set version = "2.2.27" %}
-{% set sha256 = "611cd06f1a12a543289c4fa0bbb5364bc3dbeeca905464c7c2668f45fa2fa781" %}
+{% set version = "2.2.36" %}
+{% set sha256 = "984679ca4141d74af5f1dd2537e66c68b30f0cd8a02cf8357b8209f32edc38f4" %}
 
 package:
   name: {{ name|lower }}
@@ -13,7 +13,7 @@ source:
 build:
   number: 0
   noarch: python
-  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
   run_exports:
     - {{ pin_subpackage("deeplc", max_pin="x") }}
   entry_points:
@@ -24,14 +24,10 @@ requirements:
   host:
     - python >=3.7
     - pip
-    - setuptools
   run:
     - python >=3.7
     - numpy >=1.17,<2
     - pandas >=0.25,<2
-    - matplotlib-base
-    - scipy
-    - scikit-learn
     - tensorflow >=2.2,<3
     - gooey
     - h5py
@@ -41,6 +37,7 @@ requirements:
     - psm-utils
     - hdf5plugin
     - pyopenms
+    - pyarrow
 
 test:
   imports:

recipes/difcover/0001-Replaces-fname-char-with-std-string.patch

@@ -0,0 +1,42 @@
+From e0f4ac49aa6f6d3446eed5183ea585f7bea31c34 Mon Sep 17 00:00:00 2001
+From: nikostr <[email protected]>
+Date: Fri, 31 May 2024 21:50:45 +0200
+Subject: [PATCH] Replaces fname char with std::string
+
+
+diff --git a/dif_cover_scripts/from_unionbed_to_ratio_per_window_CC0 b/dif_cover_scripts/from_unionbed_to_ratio_per_window_CC0
+old mode 100644
+new mode 100755
+index ee868ce..6c0a513
+Binary files a/dif_cover_scripts/from_unionbed_to_ratio_per_window_CC0 and b/dif_cover_scripts/from_unionbed_to_ratio_per_window_CC0 differ
+diff --git a/dif_cover_scripts/from_unionbed_to_ratio_per_window_CC0.cpp b/dif_cover_scripts/from_unionbed_to_ratio_per_window_CC0.cpp
+index 88aa296..40152a5 100644
+--- a/dif_cover_scripts/from_unionbed_to_ratio_per_window_CC0.cpp
++++ b/dif_cover_scripts/from_unionbed_to_ratio_per_window_CC0.cpp
+@@ -20,7 +20,7 @@ int main( int argc , char** argv ) {
+
+
+    int opt, a=1, A=max_cov, b=1, B=max_cov, v=1000, l=0; //!!! Default values for parameters !!!!
+-   char fname[1000], fff[1000];
++   char fff[1000];
+
+    while ((opt = getopt(argc, argv, "a:A:b:B:v:l:")) != -1) {
+         switch (opt) {
+@@ -54,12 +54,12 @@ int main( int argc , char** argv ) {
+         exit(EXIT_FAILURE);
+     }
+
+-   strncat(fname,argv[optind],strlen(argv[optind]));
++   std::string fname(argv[optind]);
+    //printf ("fname=%s\n",fname);
+
+    std::ifstream unionbed_file( fname ) ;
+    if (!unionbed_file) {
+-	fprintf(stderr, "Can't open union.bed file %s\n",fname);	
++	fprintf(stderr, "Can't open union.bed file %s\n",fname.c_str());
+         exit(EXIT_FAILURE);
+     }
+
+-- 
+2.44.0
+

recipes/difcover/build.sh

@@ -6,5 +6,5 @@ rm from_unionbed_to_ratio_per_window_CC0
 make CXX="${GXX} ${LDFLAGS}"
 
 mkdir -p "${PREFIX}/bin"
-cp from_unionbed_to_ratio_per_window_CC0 *.sh "${PREFIX}/bin"
+cp from_unionbed_to_ratio_per_window_CC0 *.R *.sh "${PREFIX}/bin"
 chmod +x ${PREFIX}/bin/*.sh

recipes/difcover/meta.yaml

@@ -5,14 +5,16 @@ package:
   version: {{ version }}
 
 build:
-  number: 0
+  number: 1
   skip: True  # [osx]
   run_exports:
     - {{ pin_subpackage("difcover", max_pin="x") }}
 
 source:
   url: https://github.com/timnat/DifCover/archive/refs/tags/v{{ version }}.tar.gz
   sha256: 52f950f35bfcd6c863127bae937da1158dd16da5c1a0e85f523561504d300447
+  patches:
+    - 0001-Replaces-fname-char-with-std-string.patch
 
 requirements:
   build:

recipes/easypqp/meta.yaml

@@ -1,6 +1,6 @@
 {% set name = "easypqp" %}
-{% set version = "0.1.42" %}
-{% set sha256 = "5f7420d350769e7bc7defbae8e48dfed270ad4ae112ba0a74b47e39fedfbbe27" %}
+{% set version = "0.1.44" %}
+{% set sha256 = "63b40374eea5518ba962dd0794cdd30e2ae19c920c87a8ed4c63df81e860fec8" %}
 
 package:
   name: {{ name|lower }}
@@ -13,11 +13,11 @@ source:
 build:
   number: 0
   noarch: python
-  script: {{ PYTHON }} -m pip install . --use-pep517 --no-deps --no-build-isolation -vvv
+  script: {{ PYTHON }} -m pip install . --no-cache-dir --no-deps --no-build-isolation -vvv
   entry_points:
     - easypqp=easypqp.main:cli
   run_exports:
-    - {{ pin_subpackage('easypqp', max_pin="x") }}
+    - {{ pin_subpackage('easypqp', max_pin="x.x") }}
 
 requirements:
   host:
@@ -36,7 +36,7 @@ requirements:
     - pyprophet
     - pyopenms
     - matplotlib-base
-    - seaborn
+    - seaborn-base
     - tqdm
 
 test: