environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: ramdaq-1.0dev
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - conda-forge::r-base
  - conda-forge::r-data.table
  - conda-forge::r-gplots
  - conda-forge::r-markdown
  - conda-forge::r-stringr
  - conda-forge::r-ggplot2
  - conda-forge::r-dplyr
  - conda-forge::r-rtsne
  - conda-forge::r-umap

  - bioconductor-edger=3.26.5
  - conda-forge::python=3.7.3
  - conda-forge::markdown=3.1.1
  - conda-forge::pymdown-extensions=6.0
  - conda-forge::pygments=2.5.2
  - bioconda::fastqc=0.11.8
  - bioconda::multiqc=1.9
  - bioconda::hisat2=2.2.0=py37h3340039_2
  - bioconda::qualimap=2.2.2d
  - bioconda::rseqc=3.0.1
  - bioconda::ea-utils=1.1.2.779
  - bioconda::samtools=1.10
  - bioconda::ucsc-wigtobigwig
  - bioconda::bamtools=2.5.1
  - bioconda::subread=2.0.1
  - bioconda::rsem=1.3.3=pl526hfbaaabd_1
  - bioconda::bowtie2=2.4.2