Motif Workflow

Simple workflow that runs MEME-Suite's MEME and TomTom in factobook-meme on entire encode datasets. Encode datasets are looked up on the fly using the ENCODE API.

Modes

Has two modes, Chip-Seq and Methyl.

Chip-Seq Mode

Chip-Seq mode runs against every released ENCODE Chip-Seq experiment.

Methyl Mode

Methyl mode runs against every released ENCODE WGBS experiment with applicable bed-methyl files.

Configuration

Krews workflows are run with a configuration file argument --config path/to/my-config.conf. Two example configurations are provided in the config directory, one for chip-seq mode and one for methyl.

Workflow Configurations

• methyl-mode - Toggles use of methyl mode if true, and chip-seq otherwise. Default value is false.

Motif Task Configurations

• methyl-percent-threshold - Percentage over which we will use a methylation site from the methylation bed file. Only useful while in methyl mode.

TomTom Task Configurations

• threshold - The TomTom threshold argument. From the docs: "Only matches for which the significance is less than or equal to the threshold set by the -thresh option (below) will be output."
• comparison-databases - A list of motif database files to compare against.

Building

Just run scripts/build.sh to build. You should find your executable Jar in build/$APP_NAME-$VERSION-exec.jar

Running

Once built, you can run scripts/run.sh with any Krews args. It's just a convenience wrapper for java -jar build/*.jar.