About Archived Tools
These tools are no longer under active development but remain available for reference and use. They represent important contributions to genomics research and may still be functional, though they may not receive updates or bug fixes. For current tools, see our active software page.
Archived Tools (13)
| Name | Description | Ecosystem | Downloads |
|---|---|---|---|
| An R package providing functions for caching R objects. Its purpose is to encourage writing reusable, restartable, and reproducible analysis pipelines for projects with massive data and computational requirements. | Standalone | | |
| Sample metadata validation and conversion tool. Eido provides an ability to take standardized metadata in PEP format and convert to any output format. It also provides a validation engine based on JSON-schema for sample metadata. | PEPkit | | |
| Refgenieserver is containerized code that hosts genome assets that can be automatically downloaded by the refgenie command-line interface. | Refgenie | | |
| A Python package providing nested attribute-style access to generic Python dictionary values. Attmap simplifies the syntax for developers of Python applications that rely on data objects. | PEPkit | | |
| Divvy is a computing resource configuration manager. It organizes your computing resources and populates job submission templates. It makes it easy for users to toggle among any computing resource (laptop, cluster, cloud). Divvy provides both an interactive Python API and a command-line interface. | PEPkit | | |
| Henge is a Python package that builds backends for generic decomposable recursive unique identifiers, providing a way to store arbitrary data, defined with JSON-schema, and uses object-derived unique identifiers to retrieve the data. | Refgenie | | |
| A small logging setup package. The point of logmuse is to make it super simple to add CLI-control of logging to your Python CLI tool. It just provides a simple interface so that standard arguments can be passed on to the logger. | Standalone | | |
| A Python package that simplifies parallel processing of DNA sequencing reads (BAM or SAM files), by parallelizing across chromosomes. Pararead is built for developers of Python scripts that process data read-by-read. It enables you to quickly and easily parallelize your script. | Standalone | | |
| A tool to provide Python and CLI interface and Python API for PEPhub. | PEPkit | | |
| A project initialization manager | PEPkit | ||
| Caravel provides a web 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. Caravel is a local web GUI for looper built with flask. | PEPkit | | |
| Pipeline for RNA-seq data. | Standalone | ||
| The seqcol package provides a Python interface to sequence collections. | Refgenie |
