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Update README.md
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jennyfothergill authored May 3, 2024
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[![pytest](https://github.com/cmelab/grits/actions/workflows/pytest.yml/badge.svg)](https://github.com/cmelab/grits/actions/workflows/pytest.yml)
[![codecov](https://codecov.io/gh/cmelab/grits/branch/main/graph/badge.svg?token=lGG8Zf65HP)](https://codecov.io/gh/cmelab/grits)
[![Documentation Status](https://readthedocs.org/projects/grits/badge/?version=latest)](https://grits.readthedocs.io/en/latest/?badge=latest)
[![Docker build](https://github.com/cmelab/grits/actions/workflows/build.yml/badge.svg)](https://github.com/cmelab/grits/actions/workflows/build.yml)

![GRiTS workflow](/.github/grits.png)

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To use GRiTS in a prebuilt container (using [Singularity](https://singularity.lbl.gov/)), run:
```bash
singularity pull docker://quay.io/cmelab/grits:latest
singularity exec grits_latest.sif bash
singularity pull docker://ghcr.io/cmelab/grits:0.4.1
singularity exec grits_0.4.1.sif bash
```

**Or** using [Docker](https://docs.docker.com/), run:
```bash
docker pull quay.io/cmelab/grits:latest
docker run -it cmelab/grits:latest
docker pull ghcr.io/cmelab/grits:0.4.1
docker run -it cmelab/grits:0.4.1
```

#### Custom install
To create a local environment with [conda](https://docs.conda.io/en/latest/miniconda.html), run:
To create a local environment with [micromamba](https://mamba.readthedocs.io/en/latest/user_guide/micromamba.html)), run:
```bash
conda env create -f environment.yml
conda activate grits
micromamba create -f environment.yml
micromamba activate grits
```
With the `grits` environment active, install the package with pip:
```
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