From b3c5cd5409b233f3f9f5911f1c9f00750cd0f356 Mon Sep 17 00:00:00 2001
From: Matthew Berkeley <42berkeley@cua.edu>
Date: Fri, 11 Oct 2024 19:17:48 +0200
Subject: [PATCH] Update busco to v5.8.0 (#51337)

* Update meta.yaml

* clean up recipe

---------

Co-authored-by: mencian <joshua.zhuang@yahoo.com>
---
 recipes/busco/build.sh  |  4 ++--
 recipes/busco/meta.yaml | 29 ++++++++++++++---------------
 2 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/recipes/busco/build.sh b/recipes/busco/build.sh
index ea804dee9d30d..a85611463c9f3 100644
--- a/recipes/busco/build.sh
+++ b/recipes/busco/build.sh
@@ -2,9 +2,9 @@
 
 set -euxo pipefail
 
-"${PYTHON}" -m pip install . --no-deps -vv
+"${PYTHON}" -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv
 
 mkdir -p $PREFIX/bin/
-cp bin/busco $PREFIX/bin/busco #python script
+cp bin/busco $PREFIX/bin/busco  #python script
 cp scripts/generate_plot.py $PREFIX/bin/generate_plot.py
 
diff --git a/recipes/busco/meta.yaml b/recipes/busco/meta.yaml
index 301a04bc398ed..02a82468a2c85 100644
--- a/recipes/busco/meta.yaml
+++ b/recipes/busco/meta.yaml
@@ -1,16 +1,16 @@
 {% set name = "busco" %}
-{% set version = "5.7.1" %}
-{% set sha256 = "d57066b68d533f0b86518653430ba47b748ef14db56d2a992601d3e26096cad6" %}
+{% set version = "5.8.0" %}
+{% set sha256 = "201218349224d35b4ad2de345505710e7778904e0f1158874b2a4d0cb2dce1ed" %}
 
 package:
   name: busco
   version: {{ version }}
 
 build:
-  number: 1
+  number: 0
   noarch: python
   run_exports:
-    - {{ pin_subpackage(name, max_pin="x.x") }}
+    - {{ pin_subpackage(name, max_pin="x") }}
 
 source:
   url: https://gitlab.com/ezlab/busco/-/archive/{{ version }}/busco-{{ version }}.tar.gz
@@ -24,13 +24,13 @@ requirements:
     - python >=3.3
     - pip
     - wget
-    - blast >=2.10.1 # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
-    - hmmer >=3.1b2 # sepp needs this version
+    - blast >=2.10.1  # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
+    - hmmer >=3.1b2  # sepp needs this version
     - augustus >=3.3
     - biopython >=1.79
     - prodigal
     - sepp >=4.3.10
-    - metaeuk >=6.a5d39d9 # needed for gff bug fix
+    - metaeuk >=6.a5d39d9  # needed for gff bug fix
     - pandas
     - bbmap
     - miniprot
@@ -38,15 +38,15 @@ requirements:
   run:
     - python >=3.3
     - wget
-    - blast >=2.10.1 # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
-    - hmmer >=3.1b2 # sepp needs this version
+    - blast >=2.10.1  # There is a multithreading problem for all BLAST versions between 2.4 and 2.10.0
+    - hmmer >=3.1b2  # sepp needs this version
     - augustus >=3.3
     - biopython >=1.79
     - r-base
     - r-ggplot2 >=2.2.1
     - prodigal
     - sepp >=4.3.10
-    - metaeuk >=6.a5d39d9 # needed for gff bug fix
+    - metaeuk >=6.a5d39d9  # needed for gff bug fix
     - pandas
     - bbmap
     - miniprot
@@ -62,16 +62,17 @@ test:
     - test_data
 
 about:
-  home: https://busco.ezlab.org/
+  home: "https://busco.ezlab.org"
   license: MIT
   license_family: MIT
   license_file: LICENSE
-  summary: Assessment of assembly completeness using Universal Single Copy Orthologs
+  summary: "Assessment of assembly completeness using Universal Single Copy Orthologs."
   description: BUSCO provides measures for quantitative assessment of genome
            assembly, gene set, and transcriptome completeness based on
            evolutionarily informed expectations of gene content from
            near-universal single-copy orthologs selected from OrthoDB.
-  dev_url: https://gitlab.com/ezlab/busco
+  dev_url: "https://gitlab.com/ezlab/busco"
+  doc_url: "https://busco.ezlab.org/busco_userguide.html"
 
 extra:
   container:
@@ -84,6 +85,4 @@ extra:
     - doi:10.1093/bioinformatics/btv351
     - usegalaxy-eu:busco
   recipe-maintainers:
-    - silask
-    - matsepp
     - berkelem