Download

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

Install

Conda

conda install bioconda::rearr

Image

Docker is built automatically by the github workflow of bioconda at https://quay.io/repository/biocontainers/rearr. Singularity is built by galaxy project at https://depot.galaxyproject.org/singularity. These images contain only necessary tools for analyes. A docker image containing webUI is at ghcr.io/ljw20180420/rearr.

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

- [ ] list bad examples in benchmark
- [ ] Write core functions in c++
- [ ] Add assumption check.
- [ ] Rewrite pruned backtracking.
- [ ] Add a simulation for branch-and-bound backtracking.
- [ ] Resemble outputs of previous software
- [ ] Use small genome data to recover genome test.
- [ ] compare with divide-and-conquer
- [ ] modulerize demultiplex
- [ ] add manim to show the core algorithm of rearr
- [ ] add method to search genome-wide off-target for sequences not found in sgRNA libraries
- [ ] add benchmark to demultiplex
- [ ] 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)
- [ ] use functools LRU-cache to speed up python code
- [ ] add benchmark for SIQ: https://github.com/RobinVanSchendel/SIQ
- [ ] add benchmark for PEM-Q: https://github.com/liumz93/PEM-Q
- [ ] convert alg to sam
- [ ] Deploy to JCloud. Celery flower does not work properly on JCloud. Maybe permission problem.
- [ ] asgi is more advance than wsgi
- [ ] resemble indelphi to explicitly list sequences
- [ ] implement tidymodels (need to install tidymodels in shiny rocker, not install by apt)
- [ ] CDN
- [ ] 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)

- [ ] Use GNU autotools to install Rearrangement
- [ ] DeepFri