26 projects
looper
A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
pipestat
A pipeline results reporter
pepdbagent
A python-based database manager for portable encapsulated projects
peppy
A python-based project metadata manager for portable encapsulated projects
bbconf
Configuration package for bedbase project
ubiquerg
Various utility functions
piper
A lightweight python toolkit for gluing together restartable, robust command line pipelines
pephubclient
PEPhub command line interface.
logmuse
Logging setup
geofetch
Downloads data and metadata from GEO and SRA and creates standard PEPs.
yacman
A standardized configuration object for reference genome assemblies
eido
A project metadata validator
cloudwatcher
A tool for monitoring AWS CloudWatch metrics
lucidoc
API documentation in Markdown
pipestat-reader
A generator of pipestat-based APIs
veracitools
Testing utilities
bulker
Manager of portable multi-container computing environments
attmap
Multiple access patterns for key-value reference
refgenie
Refgenie creates a standardized folder structure for reference genome files and indexes. You can download pre-built genomes or build your own for any fasta file
refgenconf
A standardized configuration object for reference genome assemblies
divvy
A python-based configuration manager for portable environment configurations
refgenieserver
This server provides both a web interface and a RESTful API. Users may explore and download archived indexes from the web interface or develop tools that programmatically query the API.
loopercli
A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
caravel
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.
pararead
Parallel processing of sequencing reads
ngstk
Next-generation sequencing utility functions