This small tutorial will explain to you how to install and run Sarek on a small sample test data on any POSIX compatible system (Linux, Solaris, OS X, etc).
To use this pipeline, you need to have a working version of Nextflow installed, Reference files and Docker or Singularity as a container engine. You can use a small reference genome as testing.
- See the Install Nextflow documentation
- See the Reference files documentation
- See the Install Docker documentation
- See the Install Singularity documentation
This workflow itself needs little installation.
Nextflow will automatically fetch Sarek from GitHub when launched if SciLifeLab/Sarek is specified as the workflow name.
You can also specify Nextflow to pull Sarek using:
nextflow pull SciLifeLab/SarekSarek use Singularity containers to package all the different tools.
If you plan to use the automatic pull of Singularity images, you can use the singularity.config configuration file.
You can also set up the Nextflow environnement variable NXF_SINGULARITY_CACHEDIR to choose where to store them.
For example
export NXF_SINGULARITY_CACHEDIR=$HOME/.singularityDocker can also be used as a container technology.
You can Test Sarek with small dataset and small reference
To update Sarek, it's also very simple:
# Connect to your system
> ssh -AX [USER]@[system]REFERENCES
# Or just open a terminal
# Update Sarek
> nextflow pull SciLifeLab/SarekFollow the references documentation on how to download/build the references files.
Follow the configuration and profile documentation on how to modify and use the configuration files and profiles.