Run with docker & Singularity

Docker

• Prepare input files as mentioned earlier.
• Install docker on your system. Docker Installation Instructions
• Fetch and use the needed image from dockerhub. (https://hub.docker.com/r/likelet/cirpipe/)
• Run the circPipe. Run the pipeline with the option -profile standard,docker.

Singularity

• Prepare input files as mentioned earlier.
• Run the circPipe. Run the pipeline with the option -profile standard,singularity.

An image containing all of the software requirements will be automatically fetched and used from singularity hub.

• Run offline with Singularity Download and transfer the Singularity image first:

singularity pull --name circPipe.simg shub://likelet/cirpipe

Use -with-singularity and specify the path to the image file:

nextflow run /path/to/circPipe -with-singularity circPipe.simg

Remember to pull updated versions of the singularity image when updating the pipeline.