Update assemblycomparator2 to 2.7.1 (bioconda#48242)

* Update assemblycomparator2 to 2.7.1

* clean up recipe

* add docs

---------

Co-authored-by: mencian <[email protected]>

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
-