EPI2MELabs downloads and resources
Below are listed all resources on which EPI2MELabs is built. We aim for all components of EPI2MELabs to be open source (including this website) and available through our GitHub repository: https://github.com/epi2me-labs/tutorials.
If you find something is not available please contact support@nanoporetech.com
EPI2MELabs Launcher
The LabsLauncher is used to start, stop, and update the EPI2MELabs notebook server. We provide executables for Windows 10, macOS, and Linux.
| Platform | Download |
|---|---|
| Windows 10 | ont-epi2melabs-installer-v1.0.8-win10.exe |
| macOS | ont-epi2melabs-launcher-v1.0.8-macos.dmg |
| Ubuntu 16.04 | ont-epi2melabs-launcher-1.0.8-0.xenial.deb |
| Ubuntu 18.04 | ont-epi2melabs-launcher-1.0.8-0.bionic.deb |
| Ubuntu 20.04 | ont-epi2melabs-launcher-1.0.8-0.focal.deb |
| CentOS 7 | ont-epi2melabs-launcher-1.0.8-1.el7.x86_64.rpm |
| CentOS 8 | ont-epi2melabs-launcher-1.0.8-1.el8.x86_64.rpm |
The launcher is written in Python with Qt and the sourcecode is available from GitHub: https://github.com/epi2me-labs/labslauncher.
Notebook files
A listing of all available notebooks is available on the Notebook Index page.
The notebooks used within EPI2MELabs are available in their source form from the GitHub repository: https://github.com/epi2me-labs/tutorials. These are updated regularly with enhancements and fixes.
Docker containers
The docker container for the EPI2MELabs notebook server is hosted on dockerhub: https://hub.docker.com/r/ontresearch/nanolabs-notebook, with the source code for the build process on Github: https://github.com/epi2me-labs/nanolabs.
The notebook server is based on the docker-stacks
Nextflow workflows
A listing of all available notebooks is available on the Workflows Index page.
All EPI2ME Labs workflows are available open-source through our
Github space; workflow projects
are named with a wf-artic prefix.
The workflows can be run easily using nextflow without explicitely downloading anything from Github, for example:
nextflow run epi2me-labs/wf-artic --helpWill download our SARS-CoV-2 ARTIC sequencing workflow and display its help text. See the Workflow Quick Start for further information.
Aplanat
Aplanat is a plotting library built on top of bokeh. It allows graphs to be contructed and displayed in notebooks with minimal boiler plate. Aplanat also provides functionality to generate static HTML report documents, as used in the EPI2ME Labs Nextflow workflows.
Mapula
Mapula is an alignment statistics package designed to work on streaming data; it can be inlined in a typical samtools pipeline to calculate statistic on-the-fly.
