SCING: Single-Cell pIpeliNe Garden

Pronounced as "sing" /siŋ/

Unified framework for building and running single-cell computational pipelines

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Coming Soon

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-jre

JDK (Zulu OpenJDK v11):

conda install -c conda-forge openjdk

On HPC:

module add java/11.0.12

Build 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/bin

Go to $HOME/scing/bin and extract everything:

cd $HOME/scing/bin
ls -1 *.tar.gz | xargs -I {} bash -c "tar xvzf {} && rm -rf {}"