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TrackHubGenerator

Python, CWL and Make tools for generating UCSC Track Hubs. These can be added as custom data to both the UCSC Genome Browser and the Ensembl browser.

The trackhub data generated can be found on GCB's trackhub server.

Usage

This tool is designed to operate on directories of bed files, generated by SVR_models. The bed files generated will be specific to a TF (e.g. E2F1 or E2F4) and a genome assembly (e.g. hg19 or hg38).

First, the bigbed-workflow.cwl workflow should be used to combine and convert the bed files into bigbed (.bb) files. Doing so requires CWL. A JSON job order file like bigbed-workflow-test.json is recommended:

$ export PATH=$PATH:/path/to/TrackHubGenerator/cwl/bin
$ cwltool --outdir /path/to/datadir bigbed-workflow.cwl job.json

This workflow produces a bigbed files as prescribed by the JSON.

To build the track hub directory, run make, specifying the path to the data directory (where the .bb files were placed) as well as the desired track hub directory:

  make HUBROOT=/path/to/trackhub DATA=/path/to/datadir