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fix test readme
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kdm9 committed Jan 22, 2024
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Expand Up @@ -11,30 +11,8 @@ pipelines from Acanthophis to call variants in this simulated dataset.

To run this test pipeline, one must:

### Quick mode: the core pipeline using the CI suite.

Two scripts
```bash

## Complete version

Either `bash setup.sh && bash test.sh`, or:

```bash
conda env create -f environment-setup.yml -n acanthophis-demo
conda activate acanthophis-demo
# Install Acanthophis
pip install -e ..
# 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 -j 8 --use-conda
```
1. **Generate the test dataset: `bash setup.sh`**. Uses a population genetic simulation & then read simulation to generate a fake dataset.
2. **Run the tests: `bash test.sh --quick`**. Deploys the Acanthophis pipeline, and runs a slightly reduced pipeline that requires only conda (every single step of the entire pipeline can be run by omitting `--quick`, but this can take some time)


To initialise your own workflow, [follow the main
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