environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
channels:
  - conda-forge
  - bioconda
dependencies:
  # Specify python version
  - python=2.7
  # Existing depenedencies
  - bioconda::fastqc=0.11.8
  - conda-forge::r-markdown=1.1
  - bioconda::trim-galore=0.6.4
  - bioconda::samtools=1.9
  - bioconda::bowtie2=2.3.5
  - bioconda::hisat2=2.1.0
  - bioconda::bismark=0.22.2
  - bioconda::qualimap=2.2.2c
  - bioconda::preseq=2.0.3
  - bioconda::multiqc=1.7
  - bioconda::picard=2.21.3
  - bioconda::bwameth=0.2.2
  - bioconda::methyldackel=0.4.0
  # Python-specific dependencies
  - backports=1.0
  - backports.functools_lru_cache=1.6.1
  - backports_abc=0.5
  - bz2file=0.98
  - certifi=2019.9.11
  - cffi=1.13.2
  - chardet=3.0.4
  - click=7.0
  - colormath=3.0.0
  - cryptography=2.8
  - cycler=0.10.0
  - decorator=4.4.1
  - enum34=1.1.6
  - functools32=3.2.3.2
  - future=0.18.2
  - futures=3.3.0
  - idna=2.8
  - ipaddress=1.0.23
  - jinja2=2.10.3
  - kiwisolver=1.1.0
  - markdown=3.1.1
  - markupsafe=1.1.1
  - matplotlib=2.2.4
  - matplotlib-base=2.2.4
  - networkx=2.2
  - numpy=1.16.5
  - pycparser=2.19
  - pyopenssl=19.0.0
  - pyparsing=2.4.5
  - pyqt=5.12.3
  - pysocks=1.7.1
  - python=2.7.15
  - python-dateutil=2.8.1
  - pytz=2019.3
  - pyyaml=5.1.2
  - requests=2.22.0
  - setuptools=41.6.0
  - simplejson=3.17.0
  - singledispatch=3.4.0.3
  - six=1.13.0
  - spectra=0.0.11
  - subprocess32=3.5.4
  - tornado=5.1.1
  - urllib3=1.25.7
  - wheel=0.33.6
  - xopen=0.8.4