Installation
Dependencies
The pipeline require only a UNIX system, Nextflow and either Docker or Singularity. Please, for installing these tools refer to their manual.
Downloading the pipeline
You can easily get a copy of the pipeline with:
Warning
The pipeline requires a UNIX system, therefore, Windows users may successfully use this pipeline via the Linux subsystem for window. Nextflow team has made available a nice tutorial about this issue.
Downloading docker images
The docker images used by the pipeline are:
docker pull fmalmeida/bacannot:v3.2_misc ;
docker pull fmalmeida/bacannot:v3.2_perlenv ;
docker pull fmalmeida/bacannot:v3.2_pyenv ;
docker pull fmalmeida/bacannot:v3.2_renv ;
docker pull fmalmeida/bacannot:jbrowse ;
Using singularity
Docker and singularity images are downloaded on the fly. Be sure to properly set NXF_SINGULARITY_LIBRARYDIR
env variable to a writable directory if using Singularity. This will make that the downloaded images are resuable through different executions. Read more at: https://www.nextflow.io/docs/latest/singularity.html#singularity-docker-hub
For example, to download the images for docker you may:
Testing your installation
After that, you can run the pipeline with a testing dataset by selecting one of the available profiles:
- Docker
nextflow run fmalmeida/mpgap -profile docker,test
- Singularity
nextflow run fmalmeida/mpgap -profile singularity,test
About NF profiles
Please read more about how to proper select NF profiles to better understand it.