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Update busco to v5.8.0 #51337

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merged 3 commits into from
Oct 11, 2024
Merged

Update busco to v5.8.0 #51337

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e8d6722
Update meta.yaml
berkelem Oct 11, 2024
aebdb69
Merge branch 'master' into master
berkelem Oct 11, 2024
4281fb8
clean up recipe
mencian Oct 11, 2024
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4 changes: 2 additions & 2 deletions recipes/busco/build.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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

29 changes: 14 additions & 15 deletions recipes/busco/meta.yaml
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -24,29 +24,29 @@ 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
- requests
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
Expand All @@ -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:
Expand All @@ -84,6 +85,4 @@ extra:
- doi:10.1093/bioinformatics/btv351
- usegalaxy-eu:busco
recipe-maintainers:
- silask
- matsepp
- berkelem