Installation¶

Runtime Dependencies¶

cutadapt (sequence extraction)
starcode (sequence clustering)
fastp (merging/quality filtering)
pysam (sam file conversion to fastq)

Conda¶

You may use conda, mamba, or micromamba to install pycashier and it’s runtime dependencies.

micromamba install bioconda::cutadapt bioconda::fastp bioconda::pysam bioconda::starcode conda-forge::pycashier

You can also use the included env.yml to create your environment and install everything you need.

wget https://raw.githubusercontent.com/brocklab/pycashier/main/conda/env.yml
micromamba create -f env.yml
micromamba activate cashierenv

Additionally, you may use pixi to install and use pycashier.

pixi init --channel conda-forge --channel bioconda myproject
cd myproject
pixi add pycashier starcode pysam cutadapt fastp
pixi shell

Docker¶

If you prefer to use use docker you can use the below command.

docker run --rm -it -v $PWD:/data -u $(id -u):$(id -g) ghcr.io/brocklab/pycashier

Note

You should specify a version tag with the image for better reproducibility for example, ghrc.io/brocklab/pycashier:v2024.1001.

Pip (Not Recommended)¶

You may install with pip. Though it will be up to you to ensure all the dependencies you would install from bioconda are on your path and installed correctly. At a minimum, pycashier should check that any dependencies are available on the PATH. However, it will not verify the versions installed are sufficiently recent.

pip install pycashier