mnaseseq/environment.yml at dev · sofsta/mnaseseq · GitHub

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# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: nf-core-mnaseseq-1.0dev
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  ## conda-forge packages
  - conda-forge::python=2.7.15
  - conda-forge::r-base=3.5.1
  - conda-forge::markdown=3.1.1
  - conda-forge::pymdown-extensions=6.0
  - conda-forge::pygments=2.5.2
  - conda-forge::pigz=2.3.4

  ## bioconda packages
  - bioconda::fastqc=0.11.9
  - bioconda::trim-galore=0.6.5
  - bioconda::bwa=0.7.17
  - bioconda::samtools=1.9
  - bioconda::picard=2.21.9
  - bioconda::bamtools=2.5.1
  - bioconda::pysam=0.15.4
  - bioconda::bedtools=2.29.2
  - bioconda::ucsc-bedgraphtobigwig=377
  - bioconda::ucsc-wigtobigwig=377
  - bioconda::danpos=2.2.2
  - bioconda::preseq=2.0.3
  - bioconda::deeptools=3.3.0
  - bioconda::multiqc=1.8