# This file created by conda-build 24.5.1
# meta.yaml template originally from:
# /opt/recipe, last modified Mon Jul 15 12:32:39 2024
# ------------------------------------------------

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 >=4.4.0,<5.0a0
  string: h4ac6f70_0
requirements:
  build:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - _sysroot_linux-64_curr_repodata_hack 3 h69a702a_16
    - binutils_impl_linux-64 2.40 ha1999f0_7
    - binutils_linux-64 2.40 hb3c18ed_9
    - gcc_impl_linux-64 12.3.0 h58ffeeb_13
    - gcc_linux-64 12.3.0 h9528a6a_9
    - gxx_impl_linux-64 12.3.0 h2a574ab_13
    - gxx_linux-64 12.3.0 ha28b414_9
    - kernel-headers_linux-64 3.10.0 h4a8ded7_16
    - ld_impl_linux-64 2.40 hf3520f5_7
    - libgcc-devel_linux-64 12.3.0 h6b66f73_113
    - libgcc-ng 14.1.0 h77fa898_0
    - libgomp 14.1.0 h77fa898_0
    - libsanitizer 12.3.0 hb8811af_13
    - libstdcxx-devel_linux-64 12.3.0 h6b66f73_113
    - libstdcxx-ng 14.1.0 hc0a3c3a_0
    - make 4.3 hd18ef5c_1
    - sysroot_linux-64 2.17 h4a8ded7_16
    - tzdata 2024a h0c530f3_0
  host:
    - _libgcc_mutex 0.1 conda_forge
    - _openmp_mutex 4.5 2_gnu
    - libgcc-ng 14.1.0 h77fa898_0
    - libgomp 14.1.0 h77fa898_0
    - libstdcxx-ng 14.1.0 hc0a3c3a_0
  run:
    - bedtools
    - bioconductor-bsgenome
    - bioconductor-genomeinfodb
    - bioconductor-genomeinfodbdata
    - bioconductor-plyranges
    - cd-hit
    - emboss
    - genometools-genometools
    - hmmer
    - libgcc-ng >=12
    - libstdcxx-ng >=12
    - ltr_retriever
    - mafft
    - mreps
    - ncls =0.0.64
    - ninja-nj
    - pandas
    - parallel
    - pybedtools
    - pyfaidx
    - pyranges
    - python =3.9
    - r-ape
    - r-cowplot
    - r-ggtext
    - r-optparse
    - r-plyr
    - r-tidyverse
    - r-viridis
    - recon
    - repeatmasker =4.1.5
    - repeatmodeler >=2.0.4
    - repeatscout
    - trf
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:
  copy_test_source_files: true
  final: true
  identifiers:
    - doi:10.1093/molbev/msae068
