Collection of exercises for course Population Genomics in Practice
Under construction
Create a conda environment called pgip using the environment file
conda create --name pgip python=3.9
conda activate pgip
mamba env update -f=environment.yaml
and install additional python requirements with pip
pip install -r requirements.txt
Install pgip and bash jupyter kernels
python -m bash_kernel.install
python -m ipykernel install --user --name pgip --display-name "Population Genomics in Practice (Python)"
Edit MyST markdown files and build the docs with
make
NB: once acceptable test data has been generated, relevant output is added to the git repo and there is no need to regenerate it.
Install additional data development requirements
pip install -r requirements-dev.txt
Test data can be generated in data directory as follows
cd data
./make_test_data.py
bash code cell blocks by default return garbled output - see takluyver/bash_kernel#115. The solution is to set bracketed output off. It suffices to add a code cell at the top of a notebook that runs the bash kernel:
```{code-cell} bash
:"tags": ["remove-output"]
bind 'set enable-bracketed-paste off'
```