Conda & modules
Conda
If you work with conda you can use mamba instead, which is faster tool
to install packages.
We created shared conda environments to simplify your life.
- To list all available envs:
conda env list - To activate env:
source activate brickman
Creating own shared environment
Here is an example how we created shared environment called brickman.
module load miniconda/latest
conda create --prefix /maps/projects/dan1/data/Brickman/conda/envs/brickman python=3.10
source activate brickman
pip install cruft cookiecutter
chmod -R 755 /maps/projects/dan1/data/Brickman/conda/envs/brickman
To install shared conda environment for the lab, follow the steps below.
- Create a configuration file which contains the list of packages you want
to use. Use prefix
brickman-<NGS>.yml - Populate the configuration file
- Create the conda environment
mamba env create -p /projects/dan1/data/Brickman/conda/envs/brickman-<NGS>.yml -f brickman-<NGS>.yml
Example conda environment
Configuration for brickman-chipseq environment.
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