{% set version="103.1" %}

package:
  name: ensembl-vep
  version: {{ version }}

source:
  url: https://github.com/Ensembl/ensembl-vep/archive/release/{{ version }}.tar.gz
  sha256: 3512a2c3514f7c10b0348b45bf9fe621dc691100e43f14bec48842b1e11bbf8b

build:
  number: 1
  noarch: generic
  
requirements:
  host:
    - curl
    - perl
    - perl-archive-zip
    - perl-lwp-simple
    - unzip
    - perl-dbi
  run:
    - perl
    - htslib
    - perl-bioperl >=1.7.2
    - perl-bio-db-hts >=2.11
    - perl-dbi
    - perl-dbd-mysql
    - perl-io-compress
    - perl-json
    - perl-perlio-gzip
    - perl-sereal
    - perl-set-intervaltree
    - perl-text-csv
    - unzip

test:
  commands:
    - vep --help
    - vep_convert_cache --help
    - vep_install --help
    - haplo --help
    - variant_recoder --help

about:
  home: http://www.ensembl.org/info/docs/tools/vep/index.html
  license: Apache-2.0
  summary: Ensembl Variant Effect Predictor
  description: The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

extra:
  notes: |
    This package installs only the variant effect predictor (VEP) library
    code. To install data libraries, you can use the 'vep_install' command
    installed along with it. For example, to install the VEP library for human
    GRCh38 to a directory

    vep_install -a cf -s homo_sapiens -y GRCh38 -c /output/path/to/GRCh38/vep --CONVERT

    (note that vep_install is renamed from INSTALL.pl
     to avoid having generic script names in the PATH)

    The --CONVERT flag is not required but improves lookup speeds during
    runs. See the VEP documentation for more details

    http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html
  container:
    extended-base: True

