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.
Has two modes, Chip-Seq and Methyl.
Chip-Seq mode runs against every released ENCODE Chip-Seq experiment.
Methyl mode runs against every released ENCODE WGBS experiment with applicable bed-methyl files.
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.
methyl-mode - Toggles use of methyl mode if true, and chip-seq otherwise. Default value is false.methyl-percent-threshold - Percentage over which we will use a methylation site from the methylation bed file.
Only useful while in methyl mode.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.Just run scripts/build.sh to build. You should find your executable Jar in build/$APP_NAME-$VERSION-exec.jar
Once built, you can run scripts/run.sh with any Krews args. It's just a convenience
wrapper for java -jar build/*.jar.