diff --git a/tests/README.md b/tests/README.md index 8f52902..6da71cf 100644 --- a/tests/README.md +++ b/tests/README.md @@ -17,29 +17,25 @@ conda env create -f environment-setup.yml -n acanthophis-demo conda activate acanthophis-demo # Install Acanthophis pip install -e .. -# once I put this on PyPI: -# pip install acanthophis + +# Initalise Acanthophis +acanthophis-init . # the generate the fake dataset snakemake --snakefile Snakefile.generate-rawdata -j 8 --use-conda # and run the actual test dataset -snakemake --snakefile Snakefile -j 8 --use-conda +snakemake -j 8 --use-conda ``` -To initialise your own workflow, copy `./Snakefile` and `./config.yml` to a new -directory. Establish a conda environment with some basic dependencies -(`conda create -n workflow python snakemake mamba`). Install Acanthophis (`pip -install -e $GITHUB_URL_OR_PATH_TO_CLONE_OF_ACANTOPHIS`). Then, collect your raw -data, and create at least the two metadata files (modelled after -`./data/rl2s.tsv` and `./data/samples.tsv`). Then, customise the config file -and Snakefile to match your intended pipeline. The pipeline can then be run -using something like `snakemake --snakefile Snakefile -j 8 --use-conda ---conda-frontend mamba`. +To initialise your own workflow, run `acanthophis-init` in some new directory. +Then, collect your raw data, and create at least the required metadata files +and customise the config file to match your intended pipeline. You can then run +the pipeline using something like any other snakemake file, for example +`snakemake -j 8 --use-conda`. Please follow [the documentation +](../documentation.md), which outlines this process in much more detail. -Some day soon, one will be able to do something like `acanthophis init` in some -directory for commented boilerplate to be generated in place. A real deployment would obviously skip the creation of the fake dataset, so the below files are of no use to you: