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Migrating from v2 to v3

There are major changes from v2 to v3 of MAVIS.

Tab File Headers

Tab file headers no longer start with #. Any lines starting with a pound will be treated as comments. This will apply to mavis-style inputs as well as any tab delimited reference files


MAVIS no longer uses command line arguments, config files, and environment variables for configuration. Instead all configurable settings are controlled via a single input JSON config file


MAVIS is now integrated with snakemake instead of handling its own scheduling

Reference Annotation Files

MAVIS no longer supports the previously deprecated tab-delimited format of the annotations file. If you are still using these files in your project we have provided a script to automatically convert them to the newer format in the tools directory.

python src/tools/ \
    /path/to/tab/ \
    --input_type v2-tab \

In v3 the JSON files are slightly different to support multiple translations per transcript. You old v3 files can be automatically converted to the new format with the same script

python src/tools/ \
    /path/to/json/file.json \
    --input_type v2-json \