README.md

# Pan1c_View


## Name
Pan1c_View

## Description
Report builder for [Pan1c](https://forgemia.inra.fr/alexis.mergez/pan1c).

Pan1c (Pangenome at Chromosome Scale) is a Snakemake workflow designed to simplify the construction and quality assessment of pangenome graphs. The workflow consists of splitting the overall graph construction into chromosome-level graph construction, followed by concatenation. This reduces the complexity of graph construction and exploration while enabling the use of cluster infrastructures, ultimately reducing the overall construction time.

## Demo
Coming soon...

## Installation

### Production

No installation required.

All you need to do is download the code from your web server and add the data from Pan1c to the 'project' folder.

`git clone git@forgemia.inra.fr:philippe.bardou/pan1c_view.git`

The project folder tree:
```
project/        <= put Pan1c output in a "project" directory
└── 11Ch-v1b.Pan1c_View
    ├── data
    ├── Pan1c.11Ch-v1b.assembly.json
    ├── Pan1c.11Ch-v1b.graph.json
    ├── Pan1c.11Ch-v1b.tags.json
    ├── Pan1c.11Ch-v1b.var.json
    └── Pan1c.documentation.json
```

Access the report on your webserver : `https://mywebserver.fr/pan1c_view/?id=projectid`

Replace :
- mywebserver with the name of your web server
- projectid with one of the directories in the project directories.

### Development

For development, a local lightweight HTTP server can be used to serve the pages (http://127.0.0.1:8080/):

`npx http-server .`

## Authors and acknowledgment
- Philippe Bardou (philippe.bardou@inrae.fr)
- Alexis Mergez
- Christophe Klopp

We are grateful to the genotoul bioinformatics platform Toulouse Occitanie (Bioinfo Genotoul, https://doi.org/10.15454/1.5572369328961167E12) for providing help, computing and storage resources.

## License
Pan1c View source code is distributed under the GPL3 license.