{% set name = "pgap2" %}
{% set version = "1.0.3" %}

package:
  name: {{ name|lower }}
  version: {{ version }}

source:
  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/pgap2-{{ version }}.tar.gz
  sha256: 8f4646cc17eb945885c6e2edafb73248a5d9ef21a2ca6fa6db66b2171a8b1e61

build:
  number: 0
  noarch: python
  entry_points:
    - pgap2 = pgap2.main:main
  script: {{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
  run_exports:
    - {{ pin_subpackage('pgap2', max_pin="x") }}

requirements:
  host:
    - python >=3.10
    - setuptools
    - pip
  run:
    - python >=3.10
    - biopython ==1.82
    - networkx ==3.3
    - pyfastani ==0.5.1
    - python-edlib ==1.3.9
    - loguru ==0.6.0
    - numpy ==1.23.3
    - pandas ==1.5.0
    - pyecharts ==2.0.8
    - scikit-learn ==1.1.2
    - scipy ==1.9.1
    - tqdm ==4.64.1
    - minifasta
    - tajimas_d

    - cd-hit
    - mmseqs2

    - diamond
    - blast

    - raxml-ng
    - iqtree
    - fasttree

    - muscle
    - mafft
    - perl-bio-tools-run-alignment-tcoffee

    - seqtk
    - mcl

    - miniprot
    - clipkit
    - clonalframeml

    - prodigal

    - htslib

    - r-base
    - r-ggpubr
    - r-ggrepel
    - r-dplyr
    - r-tidyr
    - r-patchwork
    - r-optparse
    - r-fastbaps

test:
  commands:
    - pgap2 -h
    - Rscript -e "library(ggpubr)"
    - Rscript -e "library(ggrepel)"
    - Rscript -e "library(dplyr)"
    - Rscript -e "library(tidyr)"
    - Rscript -e "library(patchwork)"
    - Rscript -e "library(optparse)"

about:
  home: "https://github.com/bucongfan/PGAP2"
  license: MIT
  license_family: MIT
  license_file: LICENSE
  summary: "PGAP2: a comprehensive pan-genome analysis pipeline for prokaryotic genomes."
  dev_url: "https://github.com/bucongfan/PGAP2"
