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hisplan committed Aug 31, 2021
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Expand Up @@ -10,30 +10,23 @@ Reference dataset included:
- Human reference dataset (GRCh38/Ensembl/10x) required for Cell Ranger V(D)J
- Mouse reference dataset (GRCm38/Ensembl/10x) required for Cell Ranger V(D)J


## Build Container Image

```bash
./build.sh
```
SCING (Single-Cell pIpeliNe Garden; pronounced as "sing" /siŋ/) is required for smooth and uninteruppted build process (e.g. CI/CD). For setup, please refer to [this page](https://github.com/hisplan/scing). All the instructions below is given under the assumption that you have already configured SCING in your environment.

`build.sh` can fail if the download link has expired (10x expires the Cell Ranger download link periodically). In this case, get the fresh link from https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/6.0/, and open `config.sh` and replace `${FRESH_LINK}` with the new link:
[SCING](https://github.com/hisplan/scing) installation is required

```
version="6.0.2"
vdj_ref_version="5.0"
download_url="${FRESH_LINK}"
```bash
conda activate scing

# docker related
registry="quay.io/hisplan"
image_name="cellranger"
./build.sh
```

## Push to Docker Registry

Either you can use the `docker push` command or run `push.sh` (requires [SCING](https://github.com/hisplan/scing)):

```bash
conda activate scing

./push.sh
```

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