ymp - flexible omics pipeline
YMP is an omics pipeline designed to simplify processing large numbers of read files while remaining flexible and easily extented.
YMP relies upon Bioconda to provide all necessary tools in up-to-date versions and Snakemake to handle task execution.
Please refer to the manual for more help.
Github development version
1. Install from github
- Check out repo
git clone https://github.com/epruesse/ymp.git
or (requires ssh key set up)
git clone git@github.com:epruesse/ymp.git
- Create and activate conda environment for YMP
conda env create -n ymp --file environment.yaml
source activate ymp
- Install YMP into conda environment
pip install -e .
- Check that Ymp runs
source activate ymp
ymp --help
2. Update github installation
Usually, all you need to do is a pull:
git pull
If you see errors before jobs are executed, the core requirements may have changed. Try updating the conda environment:
source activate ymp
conda env update --file environment.yaml
If something changed in setup.py, a re-install may be necessary:
source activate ymp
pip install -U -e .