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The usage menu can be viewed\nby running without any arguments, or by giving the -h/--help option\n\n``` bash\nmavis -h\n```\n\nHelp sub-menus can be found by giving the pipeline step followed by no arguments or the -h options\n\n``` bash\nmavis cluster -h\n```\n\nCommon problems and questions are addressed on the [wiki](https://github.com/bcgsc/mavis/wiki/Help-and-Frequently-Asked-Questions).\nIf you have a question or issue that is not answered there (or already a github issue) please submit\na github issue to our [github page](https://github.com/bcgsc/mavis/issues) or contact us by email at [mavis@bcgsc.ca](mailto:mavis@bcgsc.ca)\n\n## Getting Started\n\nThe simplest way to use MAVIS is via Singularity. The MAVIS docker container used\nby singularity will take care of installing the aligner as well.\n\n```bash\npip install -U setuptools pip wheel\npip install mavis_config  # also installs snakemake\n```\n\nNow you will run mavis via Snakemake as follows\n\n```bash\nsnakemake \\\n    -j \u003cMAX JOBS\u003e \\\n    --configfile \u003cYOUR CONFIG\u003e \\\n    --use-singularity \\\n    -s Snakefile\n```\n\nFor other installation options which do not use docker/singularity see the comprehensive install\ninstructions in the [user manual](https://mavis.readthedocs.io/en/latest/install)\n\n## Citation\n\nIf you use MAVIS as a part of your project please cite\n\n[Reisle,C. et al. (2018) MAVIS: Merging, Annotation, Validation, and Illustration of Structural variants. Bioinformatics.](https://doi.org/10.1093/bioinformatics/bty621)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbcgsc%2Fmavis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbcgsc%2Fmavis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbcgsc%2Fmavis/lists"}