Sydney-Informatics-Hub/cellranger-contained

Docker and Singularity workflow for running cellranger

Cell Ranger Container

Docker/Singularity image to run Cell Ranger on Centos 6.9 kernel (Ubuntu 16.04)

If you have used this work for a publication, you must acknowledge SIH, e.g: "The authors acknowledge the technical assistance provided by the Sydney Informatics Hub, a Core Research Facility of the University of Sydney."

Quickstart for Artemis

Put this repo on Artemis e.g.

cd /project/<YOUR_PROJECT>
git clone https://github.com/Sydney-Informatics-Hub/cellranger-contained.git

Then cd cellranger-contained and modify the run_artemis.pbs script and launch with qsub run_artemis.pbs.

Otherwise here are the full instructions for getting there....

How to recreate

Build with docker

Check out this repo then build the Docker file.

sudo docker build . -t nbutter/cellranger:ubuntu1604

Run with docker.

To run this, mounting your current host directory in the container directory, at /project, and execute a run on the test images (that live in the container) run:

sudo docker run -it -v `pwd`:/project nbutter/cellranger:ubuntu1604 /bin/bash -c "cellranger sitecheck > /project/sitecheck.txt"

Push to docker hub

sudo docker push nbutter/cellranger:ubuntu1604

See the repo at https://hub.docker.com/r/nbutter/cellranger

Build with singularity

export SINGULARITY_CACHEDIR=`pwd`
export SINGULARITY_TMPDIR=`pwd`

singularity build cellranger.img docker://nbutter/cellranger:ubuntu1604

Run with singularity

To run the singularity image (noting singularity mounts the current folder by default)

singularity run --bind /project:/project cellranger.img /bin/bash -c "cd "$PBS_O_WORKDIR" && export TENX_IGNORE_DEPRECATED_OS=1; cellranger sitecheck > sitecheck.txt"