{% set version = "1.0.1" %}

package:
  name: seq-seq-pan
  version: {{ version }}

source:
  url: https://gitlab.com/chrjan/seq-seq-pan/repository/v{{ version }}/archive.tar.gz
  md5: 3d2b2c835d9a7f8412551e9462202c60

build:
  number: 0
  skip: True # [osx or py27]

requirements:
  host: 
    - python

  run:
    - python
    - biopython ==1.69
    - blat ==35
    - snakemake
    - openjdk
    - argparse
    - mauvealigner ==1.2.0

test:
  commands:
    - seq-seq-pan -h > /dev/null
    - seq-seq-pan-wga --no-hooks --config workdir=$PREFIX/opt/seq-seq-pan/example/minimal genomefile=genome_list.txt outfilename=ssp_example -n > /dev/null
    - java -jar $PREFIX/opt/seq-seq-pan/java/XMFAConsensus/XMFAconsensus_majorityvote.jar -h > /dev/null
    - seq-seq-pan-consensus -h > /dev/null
    - seq-seq-pan-genomedescription -h >/dev/null

about:
  home: https://gitlab.com/chrjan/seq-seq-pan
  license: FreeBSD
  summary: seq-seq-pan is a workflow for the SEQuential alignment of SEQuences to build a PAN-genome data structure and a whole-genome-alignment.
