New and improved ChIP-seq peak calling and associated tools.

[tovahmarkowitz]

Fix #379. Fix #382. Fix #393. Fix #380.

• Cleaned up ChIPseq.snakefile, cluster.json, and standard-bin.json.
• Removed Q5MDD from InitialChIPseqQC.snakefile and cleaned up associated issues.
• Runs Macs_narrow, Macs_broad, sicer, and gem using improved metrics. Now handles PE and SE with or without input samples.
• Outputs from the peak callers run through: Homer for motif searching (defaults), uropa for annotations (against all genes including lincRNAs and not promoter focused), calculates jaccard scores comparing all samples run through the same peak caller, runs all pairwise comparisons of IDR from samples within the same group, and runs ChIPQC for peak QC metrics.

[skchronicles]

Changes approved and merged

• commit: 290b7c7a3b717343034ef13ce00b45765a10e418