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HighlanderLab / tree_seq_pipeline

Pipeline to infer tree sequences with different datasets
MIT License
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Develop installation instructions/README #5

Open gregorgorjanc opened 1 year ago

gregorgorjanc commented 1 year ago

We should write how to install all the required software, including snakemake, Python, phasing, mamba/conda environments with tsinfer, ... all versioned

For example, I ran this on my Mac to install some snakemake version

mamba create -c bioconda -c conda-forge -n snakemake snakemake-minimal                                                                                       

mamba activate snakemake
hannesbecher commented 11 months ago

Yes, we should also export the environments that are used by the pipeline, like conda list -n myCoustomEnv --explicit > myCoustomEnv.txt. Can then save these inside the repo. For this one would have to go through the rules and see which ends are used.