25 projects
bbconf
Configuration and data management tool for BEDbase
logmuse
Logging setup
peppy
A python-based project metadata manager for portable encapsulated projects
pephubclient
PEPhub command line interface.
eido
A project metadata validator
pepdbagent
A python-based database manager for portable encapsulated projects
ubiquerg
Various utility functions
refgenconf
A standardized configuration object for reference genome assemblies
looper
A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
geofetch
Downloads data and metadata from GEO and SRA and creates standard PEPs.
attmap
Multiple access patterns for key-value reference
piper
A lightweight python toolkit for gluing together restartable, robust command line pipelines
pipestat
A pipeline results reporter
yacman
A YAML configuration manager
refgenieserver
A web interface and RESTful API for reference genome assets
refgenie
Refgenie creates a standardized folder structure for reference genome files and indexes
pararead
Parallel processing of sequencing reads
cloudwatcher
A tool for monitoring AWS CloudWatch metrics
lucidoc
API documentation in Markdown
bulker
Manager of portable multi-container computing environments
ngstk
Next-generation sequencing utility functions
4 archived projects
pipestat-reader Archived
A generator of pipestat-based APIs
veracitools Archived
Testing utilities
divvy Archived
A python-based configuration manager for portable environment configurations
caravel Archived
Caravel provides aweb interface to interact with your PEP-formatted projects. Caravel lets you submit jobs to any cluster resource manager, monitor jobs, summarize results, and browse project summary web pages.
