v1.4: Merge pull request #66 from ENCODE-DCC/PIP-120-different-spp-instances

• Update bedtools to 2.26.0.
• Import more prerequisites as assets.
• Add new --use_content_md5sum option to treat content MD5-same files as if they were envelope MD5-same during accessioning.
• Add mew --spp_instance option to over-ride default instance type for spp. Using mem3_ssd1_x32 solves spp hanging problem.
• Deploy various bug fix and compatibility improvements.

v1.3: Merge pull request #53 from ENCODE-DCC/PIP-185-fix-gzip

• Upgrade MACS2 to 2.1.1.20160309
• Add fragment length estimation over-ride option
• Add bam scrubbing option
• Calculate FRiP
• Analyze unreplicated experiments by internal pseudoreplication
• Various performance and compatibility improvements

v1.1

• Make pipeline outputs deterministic by seeding the randomizer with the input
• Upgrade to spp1.14
• Use the cross-correlation fragment length estimates from corresponding true replicates rather than recalculating for each pseudoreplicate
• Many small bug-fixes and interface improvements

Production release 1.0

v1.0

Support blank peaks-only workflow (incomplete)

Histone pre-IDR peaks

RC1 for histone peak calling (non-IDR).