environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: rvfvtyping-env
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
# conda-forge packages
  - conda-forge::python=3.6
  - conda-forge::biopython=1.78 
  - conda-forge::curl=7.76.1
  - conda-forge::pandas=1.0.1
  - conda-forge::pycountry
  - conda-forge::r-argparse=2.0.3
  - conda-forge::r-base=4.0.3
  - conda-forge::r-dplyr=1.0.5
  - conda-forge::r-ggplot2=3.3.4
  - conda-forge::r-rcolorbrewer=1.1_2
  - conda-forge::r-rvcheck=0.1.8
  - conda-forge::r-tidytree=0.3.4
  - conda-forge::unzip=6.0
  
# bioconda packages
  - bioconda::bioconductor-biostrings=2.58.0
  - bioconda::bioconductor-ggtree=2.4.1
  - bioconda::bioconductor-treeio=1.14.3
  - bioconda::dendropy=4.5.2
  - bioconda::diamond=2.0.9
  - bioconda::iqtree=2.0.3
  - bioconda::mafft=7.475
  - bioconda::nextflow=20.10.0