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Michal Stolarczyk

Username    michalstolarczyk
Date joined   Joined

26 projects

pephubclient

Last released

PEPhub command line interface.

bbconf

Last released

Configuration package for bedbase project

pararead

Last released

Parallel processing of sequencing reads

piper

Last released

A lightweight python toolkit for gluing together restartable, robust command line pipelines

pipestat

Last released

A pipeline results reporter

eido

Last released

A project metadata validator

peppy

Last released

A python-based project metadata manager for portable encapsulated projects

looper

Last released

A pipeline submission engine that parses sample inputs and submits pipelines for each sample.

pepdbagent

Last released

A python-based database manager for portable encapsulated projects

geofetch

Last released

Downloads data and metadata from GEO and SRA and creates standard PEPs.

ubiquerg

Last released

Various utility functions

logmuse

Last released

Logging setup

yacman

Last released

A standardized configuration object for reference genome assemblies

cloudwatcher

Last released

A tool for monitoring AWS CloudWatch metrics

lucidoc

Last released

API documentation in Markdown

pipestat-reader

Last released

A generator of pipestat-based APIs

veracitools

Last released

Testing utilities

bulker

Last released

Manager of portable multi-container computing environments

attmap

Last released

Multiple access patterns for key-value reference

refgenie

Last released

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

Last released

A standardized configuration object for reference genome assemblies

divvy

Last released

A python-based configuration manager for portable environment configurations

refgenieserver

Last released

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

Last released

A pipeline submission engine that parses sample inputs and submits pipelines for each sample.

caravel

Last released

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

Last released

Next-generation sequencing utility functions

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