Fish Risk Tree

A bioinformatics pipeline for generating phylogenetic trees annotated with IUCN risk status for fish taxon. Tree's with annotations are created using the NHX format.

Pipeline Parameters

Provide the runtime parameters to the pipeline as JSON:

{
    "Taxon": <See bold systems for available taxon and names>
    "Marker": <See bold systems for available markers>
    "NumBootstraps": <The number of bootstraps to use with raxml. 0 to disable bootstraps>
    "DataDirectory": <The path where all data will be stored in>
    "MuscleBinaryPath": <path to the muscle binary>
    "RaxmlBinaryPath": <path to the RAxML binary>
    "FishIucnFinderBinaryPath": <path to fish_iucn_finder.pl>
    "Seed": <Randomization seed>
    "Threads": <The number of cpu threads to run with. 0 to autodetect>
}

Running the Pipeline via CLI (RECOMMENDED)

To run the pipeline, generate a valid configuration file and run using the following:

docker run -it --rm -v <PATH TO SAVE TO LOCALLY>:<PATH TO DATA DIRECTORY IN CONFIG> llalon/fish-risk-tree:latest

run_pipeline.sh config.json

Running the Pipeline via GUI

A web GUI is also provided and can be accessed using docker:

docker run -d -p 8080:80 -v out:/out llalon/fish-risk-tree:gui-latest

Limitations

• Does not support sub species (returns NA)
• Sequence data limited to Bold Systems
• IUCN data limited to FishBase