Quickstart Demo

Run a quick demo of BATCHIE on a toy dataset.

Install the BATCHIE package in a local Python3 virtual environment:

python3 -m venv venv
source venv/bin/activate
pip install git+https://github.com/tansey-lab/batchie

Execute the retrospective-mode demo (For explanation of what retrospective-mode means see Retrospective)

python3 nextflow/scripts/batchie.py \
    --mode retrospective \
    -c nextflow/tests/config/integration_test_retrospective_simulation.config \
    --batch-size 3 \
    --screen nextflow/tests/data/unmasked_screen.h5 \
    --outdir retrospective_sim \
    --n_chains 2 \
    --n_chunks 2 \
    --max_cpus 1 \
    --max_mem 1GB \
    -profile local

On the author’s an Apple M1 13” MacBook Pro (2020) with 16GB of RAM, this command took 45.887 seconds to execute.

Execute the prospective-mode demo (For explanation of what prospective-mode means see Prospective):

python nextflow/scripts/batchie.py \
    --mode prospective \
    -c nextflow/tests/config/integration_test_retrospective_simulation.config \
    --batch-size 3 \
    --screen nextflow/tests/data/masked_screen.h5 \
    --outdir prospective_sim \
    --n_chains 2 \
    --n_chunks 2 \
    --max_cpus 1 \
    --max_mem 1GB \
    -profile local

On the author’s an Apple M1 13” MacBook Pro (2020) with 16GB of RAM, this command took 29.687 seconds to execute.