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https://github.com/LooseLab/bulkVis
https://github.com/LooseLab/bulkVis
Last synced: 3 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/LooseLab/bulkVis
- Owner: LooseLab
- License: mit
- Created: 2018-01-25T15:59:31.000Z (almost 7 years ago)
- Default Branch: 2.0
- Last Pushed: 2023-06-28T10:41:27.000Z (over 1 year ago)
- Last Synced: 2024-05-22T15:32:19.762Z (6 months ago)
- Language: Python
- Size: 1.36 MB
- Stars: 46
- Watchers: 6
- Forks: 8
- Open Issues: 20
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-microbes - BulkViz - [Python] - An app written in Python3 using Bokeh to visualise raw squiggle data from Oxford Nanopore Technologies (ONT) bulkfiles. See the documentation at https://bulkvis.readthedocs.io . (Long-read Sequencing Tools)
README
⇜ bulkvis ⇝
============
An app written in Python3 using [Bokeh][1] to visualise raw squiggle data from Oxford Nanopore Technologies (ONT) bulkfiles.
Quickstart
==========
Our preferred installation method uses `conda` with this environment setup:
```yaml
name: bulkvis
channels:
- bioconda
- conda-forge
- defaults
dependencies:
- python=3.11
- pip
- pip:
- git+https://github.com/LooseLab/[email protected]
```
Either copy the YAML above into a file or:
```console
curl -O https://raw.githubusercontent.com/LooseLab/bulkvis/2.0/env.yml
conda env create -f env.yml
```
Then bulkvis can be started using:
```console
conda activate bulkvis
bulkvis serve --show
```
or with another python source
```bash
# Make a python3 virtual environment
python3 -m venv bulkvis
# Activate virtual environment
source bulkvis/bin/activate
# Clone the repo to your installation/projects directory
pip install git+https://github.com/LooseLab/[email protected]
# Start bokeh server
bulkvis serve --show
```
Other install requires:
===
To open some bulk FAST5 files [`vbz compression plugins`][2] are required.
These are written and maintained by Oxford Nanopore Technologies.
[1]: https://github.com/bokeh/bokeh/
[2]: https://github.com/nanoporetech/vbz_compression