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Conda

To install shared conda environment for the lab, follow the steps below.

  1. Create a configuration file which contains the list of packages you want to use. Use prefix brickman-<NGS>.yml
  2. Populate the configuration file
  3. Create the conda environment
mamba env create -p /projects/dan1/data/Brickman/conda/envs/brickman-<NGS>.yml -f brickman-<NGS>.yml

Example case

Configuration for brickman-chipseq environment.

brickman-chipseq.yml
name: brickman-chipseq
channels:
  - conda-forge
  - bioconda
  - anaconda
  - defaults
dependencies:
  - bioconda::bedtools==2.31.0
  - bioconda::deeptools==2.31.0
  - bioconda::homer==4.11
  - bioconda::intervene==0.6.4
  - bioconda::macs2==2.2.9.1
  - bioconda::pygenometracks==3.8
  - bioconda::seacr==1.3
  - bioconda::samtools==1.17
prefix: /projects/dan1/data/Brickman/conda/envs/brickman-chipseq

To install the environment, run

mamba env create -p /projects/dan1/data/Brickman/conda/envs/brickman-chipseq -f brickman-chipseq.yml