HiCT

Combines all HiCT-related repositories as submodules

How to test-drive HiCT

Thanks to the GitHub Actions and Container Registry, you can try out HiCT even without cloning this repository by using autogenerated Docker images. If you do not have Docker installed, check this or use a single-liner:

curl -fsSL get.docker.com -o get-docker.sh && sh get-docker.sh

Assuming you now have Docker installed, launch this command in your terminal:

docker run \
  --mount type=bind,source=/path/to/the/data,target=/app/data \
  -p 8080:80/tcp \
  -p 5000:5000/tcp \
  --pull always \
  ghcr.io/ctlab/hict-full:latest

• You have to change /path/to/the/data to actual absolute path where you store your Coolers, AGPs, FASTAs and .hict.hdf5 files (you can store all these files in the subdirectories of that folder).
• You can change port 8080 to any other, that's the port where your WebUI will be available from host (whereas 80 is the port inside docker container and should not be changed).
• Port 5000 is used for communications between WebUI and Server, you can change that but remember to set new port in WebUI (Connection Settings at the top of the page).
• --pull always ensures that the latest version with latest tag is actually being launched (only difference will be pulled if it was changed slightly from version already present on your machine).

After running this command, open your web browser and navigate to the http://localhost:8080, WebUI should open.

How to properly clone this repository

All HiCT-related repositories are added as git submodules, so in order to properly initialize them, you need to add --recurse-submodules option to your command like: git clone --recurse-submodules https://github.com/ctlab/HiCT.git (via HTTPS) or git clone --recurse-submodules git@github.com:ctlab/HiCT.git (via SSH).

If you have already cloned repository without submodules, run git submodule update --init --recursive at the root of this cloned repository.