environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: bact_seq-1.0.0
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  ## conda-forge packages
  - conda-forge::numpy>=1.21
  - conda-forge::python>=3.7, <3.9
  - conda-forge::gawk>=5.1
  - conda-forge::pigz>=2.3 ## Required for TrimGalore multi-threading
  - conda-forge::pandas>=1.4
  - conda-forge::r-base>=3.6
  - conda-forge::r-optparse>=1.7
  - conda-forge::r-rcolorbrewer>=1
  - conda-forge::r-reshape2>=1.4
  - conda-forge::r-pheatmap>=1.0
  - conda-forge::r-matrixstats>=0.6
  - conda-forge::r-ape>=5.0
  - conda-forge::r-xtable>=1.8
  - conda-forge::r-rsqlite>=2.2
  - conda-forge::r-plyr>=1.8
  - conda-forge::r-fastmap>=1.1
  - conda-forge::r-devtools>=2.4
  - conda-forge::r-scales>=1.1
  - conda-forge::r-tidyverse>=1.9

  ## bioconda packages
  - bioconda::fastqc>=0.11
  - bioconda::trim-galore>=0.6
  - bioconda::bwa>=0.7
  - bioconda::samtools>=1.15
  - bioconda::bioconductor-edger>=3.36
  - bioconda::bioconductor-deseq2>=1.34
  - bioconda::bioconductor-topgo>=2.00
  - bioconda::bioconductor-go.db>=3.00
  - bioconda::bioconductor-rsubread>=2.00
  - bioconda::bioconductor-enhancedvolcano>=1.00