pvdb90/drop-seq-tools repository overview

I use this image as base for a Singularity image: https://singularity-hub.org/collections/343/⁠ (This singularity image is configured for the cluster I use). The docker image has $picard and $dropseq environment variables pointing to the corresponding folders.

Run a STAR command (mounting current directory as working directory) docker run -it --name dropseq -v $(pwd):/home/drop-seq pvdb90/drop-seq-tools STAR <COMMAND>'

Run a picard command (mounting current directory as working directory) docker run -it --name dropseq -v $(pwd):/home/drop-seq pvdb90/drop-seq-tools bash -c 'java -jar $picard <COMMAND>'

Run a drop-seq-tools (alignment) command (mounting current directory as working directory) docker run -it --name dropseq -v $(pwd):/home/drop-seq pvdb90/drop-seq-tools bash -c '$dropseq/Drop-seq_alignment.sh <COMMAND>' Other programs from the drop-seq tool box can be run in a similar fashion