package:
  name: bcbio-nextgen
  version: '1.1.2a'

build:
  number: 1
  skip: true # [not py27]

source:
  #url: https://pypi.io/packages/source/b/bcbio-nextgen/bcbio-nextgen-1.1.1.tar.gz
  url: https://github.com/bcbio/bcbio-nextgen/archive/3a2e565.tar.gz
  sha256: cec1148e2f3411aaee84047fb4c83a545bc3863ae8f770be1e85844854b2ba39

requirements:
  host:
    - python
    - setuptools
    - pip
  run:
    - python
    - arrow
    - beautifulsoup4
    - bioblend
    - biopython
    - boto
    - cython
    - cyvcf2
    - dnapi
    - fabric
    - fadapa
    - geneimpacts
    - gffutils
    - h5py
    - htslib
    - ipyparallel >=6.0.2
    - ipython-cluster-helper >=0.6.1
    - joblib >=0.12
    - logbook
    - matplotlib
    - mock
    - msgpack-python
    - openssl
    - pandas
    - pip
    - py
    - pycrypto
    - pytest
    - pytest-cov >=2.5.1
    - pytest-mock
    - progressbar
    - psutil
    - python-dateutil >=2.5.0
    - pybedtools
    - pysam >=0.13.0
    - pyvcf
    - pyyaml
    - requests
    - scipy
    - seaborn
    - seqcluster
    - statsmodels
    - tabulate
    - toolz
    - yamllint

test:
  imports:
    - bcbio.distributed.multi
    - bcbio.pipeline.main
    - bcbio.provenance.do
    # causes failure on OSX
    # ImportError: dlopen(zmq/backend/cython/constants.so, 2): Library not loaded: @rpath/./libzmq.4.dylib
    #   Referenced from: /zmq/backend/cython/constants.so
    #     Reason: image not found
    - bcbio.distributed.ipython # [not osx]
  commands:
    # click requires a unicode locale
    - LANG=C.UTF-8 bcbio_nextgen.py -h
    - LANG=C.UTF-8 bcbio_setup_genome.py -h
    - LANG=C.UTF-8 bcbio_prepare_samples.py -h

about:
  home: https://github.com/chapmanb/bcbio-nextgen
  license: MIT
  summary: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

extra:
  identifiers:
    - biotools:bcbio-nextgen
    - doi:10.1093/bioinformatics/btv061
