package:
  name: earlgrey
  version: 4.4.0
source:
  sha256: 2557e79c112fdb2e9f1fd96d21394752db0a8004723fe35953d6619c887dcf97
  url: https://github.com/TobyBaril/EarlGrey/archive/refs/tags/v4.4.0.tar.gz
build:
  number: '0'
  run_exports:
    - earlgrey
requirements:
  build:
    - make
    - gxx_linux-64 12.*
  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:
  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.

    '
  dev_url: https://github.com/TobyBaril/EarlGrey
  doc_url: https://github.com/TobyBaril/EarlGrey/blob/main/README.md
  home: https://github.com/TobyBaril/EarlGrey
  license: OSL-2.1
  license_file: LICENSE
  summary: 'Earl Grey: A fully automated TE curation and annotation pipeline'
extra:
  final: false
  identifiers:
    - doi:10.1093/molbev/msae068
