SCING: Single-Cell pIpeliNe Garden
Pronounced as "sing" /siŋ/
Unified framework for building and running single-cell computational pipelines
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| Pipeline | Description | Version |
|---|---|---|
| SEQC | Single-cell & Single-nucleus RNA-seq 3' Preprocessor | 0.2.11 |
| SEQC Ada | SEQC AutomateD Analysis | 0.0.4 |
| Sharp (♯) | Demultiplexing Hashtag, CITE-seq, CellPlex, and ASAP-seq | 0.1.1 |
| Velopipe | RNA Velocity for SEQC | 0.0.9 |
| FastQC | A high throughput sequence QC analysis tool | 0.11.9 |
| Transgenes | Creating a reference package with transgenes | 0.0.8 |
| Cell Ranger GEX | Single-cell gene expression (3' and 5') | 6.1.2 |
| Cell Ranger V(D)J | Single-cell immune profiling (TCR/BCR) | 6.1.2 |
| Cell Ranger ATAC | Single-cell chromatin accessbility (ATAC) | 2.1.0 |
| Cell Ranger ARC | Single-cell multiome ATAC + Gene Expression | 2.0.0 |
| Space Ranger | Single-cell spatial gene expression | 1.3.1 |
| CellPlex | Cell multiplexing | 6.1.2 |
| mkref | Creating a human+mouse hybrid genome | 0.0.6 |
| ArchR | Processing and analyzing single-cell ATAC-seq data | 0.1.0 |
Coming Soon
| Pipeline | Description |
|---|---|
| Mito Tracing | Lineage tracing using mitochondrial mutations |
Prerequisites
To use SCING, you need:
- Cromwell: a workflow management system for scientific workflows developed by the Broad Institute
- Amazon Web Services, Google Cloud Platform, Microsoft Azure, or HPC (with LSF, Slurm, ...)
If you need information about how to install Cromwell on Cloud/HPC, please follow the instructions below:
- Amazon Web Services
- Amazon Genomics Workflow: https://github.com/hisplan/cromwell-gwf-setup
- Amazon Genomics CLI (AGC): TBD
- Google Cloud Platform: TBD
- Microsoft Azure: TBD
- HPC with LSF: TBD
Install CLI (Command-Line Interface)
conda create -n scing python=3.8 pip
conda activate scing
git clone https://github.com/hisplan/scing.git
cd scing
pip install .If you are a developer of SCING, additionally install either JRE or JDK. Here are some options for installing JRE or JDK:
JRE (Java 8 packaged by Cyclus):
conda install -c cyclus java-jreJDK (Zulu OpenJDK v11):
conda install -c conda-forge openjdkOn HPC:
module add java/11.0.12Build Containers
All the required docker containers are pre-built and publicly available/accessible via quay.io/hisplan, thus building the containers are optional. If you want to build the docker containers on your own and push them to your own docker registry, please follow the instructions here. Otherwise, skip to the Install section.
Install Pipelines
Run the following command to install all the pipelines:
scing install --config=config.yaml --home $HOME/scing/binGo to $HOME/scing/bin and extract everything:
cd $HOME/scing/bin
ls -1 *.tar.gz | xargs -I {} bash -c "tar xvzf {} && rm -rf {}"
