Download

https://github.com/ljw20180420/sx_lcy/releases

Install

Native

It is recommanded to use rearr in docker. If you want to install natively, then in the project folder, execute

sudo ./install.md core sx

Docker

1. Install docker engine here.
2. Install rootless docker here.
3. Configure the proxy of docker daemon if necessary here.
4. Allow rootless docker to access loopback (e.g. local proxy listening at localhost) if necessary here.
5. Login into a tempary container.

./loginWorker.md

6. Just use as natively.

Setup web server

The web server is containerized by docker. In the project folder, execute

./compose.md

Usage

See rearrTest.md.

Documentation

Here.

TODO

- [ ] docker unit tests
- [ ] github action to deploy to qiangwulab.sjtu.edu.cn
- [ ] add github wiki
- [ ] other CDCI support by github (git -> github cli -> github docs|skills|support|community)
- [ ] add benchmark for SIQ: https://github.com/RobinVanSchendel/SIQ
- [ ] convert alg to sam
- [ ] kvm
- [ ] vue -> uniapp -> tauri2
- [ ] Deploy to JCloud. Celery flower does not work properly on JCloud. Maybe permission problem.
- [ ] asgi is more advance than wsgi
- [ ] resemble indelphi
- [ ] implement tidymodels (need to install tidymodels in shiny rocker, not install by apt)
- [ ] CDN
- [ ] Add 3D structure prediction shiny App
- [ ] Add large language model for DNA
- [ ] Use explicit base in shiny app microHomology
- [ ] Use probability language to inplement Gibbs sampling for predicting the frequencies of blunt end cleavage events

TODO (Long term)

- [ ] 4C normalization algorithm
- [ ] Use GNU autotools to install Rearrangement
- [ ] Hi-C apps
- [ ] DeepFri
- [ ] PDB structure prediction
- [ ] molecular dynamics simulation
- [ ] Call TADs