# This file created by conda-build 24.7.1
# meta.yaml template originally from:
# /opt/recipe, last modified Sat May  3 00:33:32 2025
# ------------------------------------------------

package:
  name: pgap2
  version: 1.0.3
source:
  sha256: 8f4646cc17eb945885c6e2edafb73248a5d9ef21a2ca6fa6db66b2171a8b1e61
  url: https://pypi.org/packages/source/p/pgap2/pgap2-1.0.3.tar.gz
build:
  entry_points:
    - pgap2 = pgap2.main:main
  noarch: python
  number: '0'
  run_exports:
    - pgap2 >=1.0.3,<2.0a0
  script: /opt/conda/conda-bld/pgap2_1746232595766/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/bin/python
    -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir
  string: pyhdfd78af_0
requirements:
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - bzip2 1.0.8 h4bc722e_7
    - ca-certificates 2025.4.26 hbd8a1cb_0
    - ld_impl_linux-64 2.43 h712a8e2_4
    - libexpat 2.7.0 h5888daf_0
    - libffi 3.4.6 h2dba641_1
    - libgcc 14.2.0 h767d61c_2
    - libgcc-ng 14.2.0 h69a702a_2
    - libgomp 14.2.0 h767d61c_2
    - liblzma 5.8.1 hb9d3cd8_0
    - libmpdec 4.0.0 h4bc722e_0
    - libsqlite 3.49.1 hee588c1_2
    - libuuid 2.38.1 h0b41bf4_0
    - libzlib 1.3.1 hb9d3cd8_2
    - ncurses 6.5 h2d0b736_3
    - openssl 3.5.0 h7b32b05_1
    - pip 25.1 pyh145f28c_0
    - python 3.13.3 hf636f53_101_cp313
    - python_abi 3.13 7_cp313
    - readline 8.2 h8c095d6_2
    - setuptools 80.1.0 pyhff2d567_0
    - tk 8.6.13 noxft_h4845f30_101
    - tzdata 2025b h78e105d_0
  run:
    - biopython ==1.82
    - blast
    - cd-hit
    - clipkit
    - clonalframeml
    - diamond
    - fasttree
    - htslib
    - iqtree
    - loguru ==0.6.0
    - mafft
    - mcl
    - minifasta
    - miniprot
    - mmseqs2
    - muscle
    - networkx ==3.3
    - numpy ==1.23.3
    - pandas ==1.5.0
    - perl-bio-tools-run-alignment-tcoffee
    - prodigal
    - pyecharts ==2.0.8
    - pyfastani ==0.5.1
    - python >=3.10
    - python-edlib ==1.3.9
    - r-base
    - r-dplyr
    - r-fastbaps
    - r-ggpubr
    - r-ggrepel
    - r-optparse
    - r-patchwork
    - r-tidyr
    - raxml-ng
    - scikit-learn ==1.1.2
    - scipy ==1.9.1
    - seqtk
    - tajimas_d
    - tqdm ==4.64.1
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:
  dev_url: https://github.com/bucongfan/PGAP2
  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.'
extra:
  copy_test_source_files: true
  final: true
