26 projects
pephubclient
PEPhub command line interface.
bbconf
Configuration package for bedbase project
pararead
Parallel processing of sequencing reads
piper
A lightweight python toolkit for gluing together restartable, robust command line pipelines
pipestat
A pipeline results reporter
eido
A project metadata validator
peppy
A python-based project metadata manager for portable encapsulated projects
looper
A pipeline submission engine that parses sample inputs and submits pipelines for each sample.
pepdbagent
A python-based database manager for portable encapsulated projects
geofetch
Downloads data and metadata from GEO and SRA and creates standard PEPs.
ubiquerg
Various utility functions
logmuse
Logging setup
yacman
A standardized configuration object for reference genome assemblies
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.
ngstk
Next-generation sequencing utility functions
