Run with containers¶

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.

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

Note

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
```

Note

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