{% set name = "EarlGrey" %}
{% set version = "4.4.0" %}
{% set sha256 = "2557e79c112fdb2e9f1fd96d21394752db0a8004723fe35953d6619c887dcf97" %}

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

source:
  url: https://github.com/TobyBaril/EarlGrey/archive/refs/tags/v{{ version }}.tar.gz
  sha256: {{ sha256 }}

build:
  number: 0
  run_exports:
    - {{ pin_subpackage('earlgrey', max_pin='x') }}

requirements:
  build:
    - make
    - {{ compiler('cxx') }}
  run:
    - python =3.9
    - hmmer
    - trf
    - cd-hit
    - genometools-genometools
    - pandas
    - ncls =0.0.64
    - pyfaidx
    - pyranges 
    - parallel
    - repeatmasker =4.1.5
    - ltr_retriever
    - mafft
    - mreps
    - ninja-nj
    - repeatscout
    - recon
    - repeatmodeler >=2.0.4
    - bioconductor-genomeinfodb
    - bioconductor-genomeinfodbdata
    - bioconductor-bsgenome
    - bioconductor-plyranges
    - r-ape
    - r-optparse
    - r-tidyverse
    - r-plyr
    - r-viridis
    - r-cowplot
    - r-ggtext
    - bedtools
    - emboss
    - pybedtools

test:
  commands:
    - df -h
    - earlGrey -h

about:
  home: "https://github.com/TobyBaril/EarlGrey"
  dev_url: "https://github.com/TobyBaril/EarlGrey"
  doc_url: "https://github.com/TobyBaril/EarlGrey/blob/main/README.md"
  license: OSL-2.1
  license_file: LICENSE
  summary: "Earl Grey: A fully automated TE curation and annotation pipeline"
  description: |
    Earl Grey is a full-automated transposable element (TE) annotation pipeline,
    leveraging the most widely-used tools and combining these with a consensus
    elongation process (BEAT) to better define de novo consensus sequences when
    annotating new genome assemblies.
    
extra:
  identifiers:
    - doi:10.1093/molbev/msae068
