{"id":13756398,"url":"https://github.com/SouthGreenPlatform/panache","last_synced_at":"2025-05-10T03:32:00.398Z","repository":{"id":43846792,"uuid":"346054717","full_name":"SouthGreenPlatform/panache","owner":"SouthGreenPlatform","description":"Panache is a web-based interface designed for the visualization of linearized pangenomes. 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It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.\n\n![Snapshot of banana data in Panache](imagesReadMe/panacheBanana_clipped.png?raw=true \"Banana data in Panache\")\n\n## Live demo\nAn instance of Panache is currently running at [https://panache.ird.fr/](https://panache.ird.fr/) where anyone can upload its own data.\n\nTo see an instance with an existing dataset (Banana Pangenome by Rijzaani H. et al, 2021), you can visit the [Banana Genome Hub](https://banana-genome-hub.southgreen.fr/content/panache).\n\n## Citation\nÉloi Durant, François Sabot, Matthieu Conte, Mathieu Rouard, Panache: a web browser-based viewer for linearized pangenomes, Bioinformatics, Volume 37, Issue 23, 1 December 2021, Pages 4556–4558, https://doi.org/10.1093/bioinformatics/btab688\n\n## Installation\n\n### With Docker\n\nPanache comes with a Docker container. Please make sure your machine already have Docker and Docker-compose (version \u003e= 1.10) installed. If not, you might install it using ```apt install docker docker-compose```.\n\n**!CAUTION!** Somehow the installation does not work with the \"bullseye\" distribution of debian, to correct related bugs you can modify the `Dockerfile` and in the first line replace `FROM debian` with `FROM debian:buster`. Then proceed as follows:\n\nAfter cloning Panache's repository, the container can be built and launched running ```bash start.sh``` (with your sudo rights enabled; this will both create a build version and serve it with nginx).\n\n**The web interface will be available after 4-ish minutes once everything is built.** If you are impatient and want to see what is happening live, you can also run the same command that is in ```start.sh``` without the ```-d``` option, which hides the standard output from the generated container.\nAccess the visualization through your [localhost](localhost:8080/) (by default a dev version will be served throught port 8080 and a prod version through port 1337).\n\nThe visualization could be served on a custom IP when specified inside the nginx.conf file, instead of (or alongside with) localhost.\n\n### Without Docker\n\nIf you wish to use another web server directly with the production version of files instead, you will have to run ```npm install```, followed with ```npm install @vue/cli```. Finally make sure to run ```npm run build``` to have the production version files available, they will be all stored in the directory called 'dist', ready to be served.\n\n## Main features and documentation\n\n![Animated GIF introducing the main features of Panache](imagesReadMe/panacheScreencast.gif?raw=true \"Panache Screencast\")\n\nPanache offers an interactive view of a presence/absence matrix of genomes and 'pangenome blocks'---such blocks being either sequences or gene. This matrix can be explored similarly to genome browsers, by clicking on the desired location on the miniature.\n\nMore descriptive documentation (FAQ, feature description, linearization...) is available at Panache's [wiki](https://github.com/SouthGreenPlatform/panache/wiki).\n\n## Representation\nPanache was built to display linear representations of pangenomes instead of graph-like display.\nWith every block ordered on a single string, it becomes easier to parse the representation with human eyes and makes sense of per-node data. It also makes a good baseline for additional information or metadata, that can be layed out on dedicated spaces without overloading the rest of the visualization.\n\n![Visual explanation of pangenome linearization](imagesReadMe/pangenomeLinearization.png?raw=true \"Pangenome linearization\")\n\n## Data inputs\nFile examples can be find in the `public` folder, and detailed information are available in the [Files and Formats](https://github.com/SouthGreenPlatform/panache/wiki/Files-\u0026-formats) section of the wiki\n\n## Full Documentation\n\nSee the [Wiki](https://github.com/SouthGreenPlatform/panache/wiki) for full documentation, examples and other information.\n\n## Acknowledgement\n\nPanache would not have come to light without the help of Romain Basset (transition to Vue JS framework), Mel Florance (Docker container and various enhancements) and Alexandre Bousquet (Various improvements and Sorting options for the genomes).\nThank you to Gaetan Droc for setting up Panache on the Banana Genome Hub and Philipp Bayer for his hard-won version of wheat_panache.\n\n## License\nPanache is published under the terms of the [MIT LICENSE](./LICENSE)\n\n## Contact\nEloi Durant or Mathieu Rouard\n\n---\n\n## Miscellaneous\n\u003e ***panache***, noun\n\u003e 1. an ornamental tuft (as of feathers) especially on a helmet  \n\u003e *The palace guard had a panache on his helmet.*\n\u003e\n\u003e 2. dash or flamboyance in style and action  \n\u003e *flashed his … smile and waved with the* panache *of a big-city mayor.* — Joe Morgenstern\n\n*Definition from Merriam-Webster*\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FSouthGreenPlatform%2Fpanache","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FSouthGreenPlatform%2Fpanache","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FSouthGreenPlatform%2Fpanache/lists"}