Portable Encapsulated Projects

geofetch

Builds a PEP from SRA or GEO accessions

peppy

Project metadata manager for PEPs in Python

looper

A job submitter for Portable Encapsulated Projects

pephub

A web API and database for biological sample metadata

pepspec

Documentation for PEP specification and all PEPkit software

attmap

Key-value mapping that supports nested attribute-style access

divcfg

DIvvy computing configuration files.

divvy

Standardized computing resource configuration

eido

Validator for PEP objects

pipestat

Pipeline results reporting package

pephubclient

A tool to provide Python and CLI interface and Python API for PEPhub.

pepr

Project metadata manager for PEPs in R

BiocProject

BiocProject provides a PEP-compatible R package for autoloading biological data

pepdbagent

Database for storing sample metadata

pep-cwl

pepembed

hello_looper

A Hello World! example repository for looper

example-pephub-cli

example-pephub-spa

example_peps

Some simple examples of PEP-compatible projects

geopephub

Automatic uploader of GEO metadata to PEPhub.

pep-nextflow

pep-pipelines

Examples of how to use PEP to run pipelines with different workflow systems

pep-snakemake

Example simple and bioinformatic pipelines using PEPs and snakemake.

pephub-ui

pephub.databio.org

Data stores for pephub PEPs

pepingester

pifaces

A collection of looper pipeline interfaces for common tasks

pipestat_reader

web API generator for pipeline results

ubiquerg

Tools for work (erg) everywhere (ubique)