README

HiC-3DViewer is an interactive web-based tool designed to provide an intuitive environment for investigators to facilitate the 3D exploratory analysis of Hi-C data. It contains many useful visualization and annotation functionalities.

The user manual and description of the installation details can be consulted at : HiC3DViewer/hicViewer/static/data/

Downloading the repository

You can directly clone the repository using:

    git clone https://github.com/mohamed-amine-guerras/HiC3DViewer.git

To run the HiC-3DViwer you need first to make sure that all the depencies are installed

   cd hic3dviewer/
   pip install -r requirements.txt

Run HiC-3DViwer using python directly

You can then specify autoapp.py as our entry point.

• In Windows

   set FLASK_APP=autoapp.py
   flask run -h 0.0.0.0

• In unix

   export FLASK_APP=autoapp.py
   flask run -h 0.0.0.0

In your browser go to localhost:5000 if you are running it in own computer or <serverip>:5000 if you are running in a server whith an ip serverip.

Using the docker image

Because some users had some dificulties running HiC-3DViewer and because I don't have acess to the web-version on Tsinghua server, I created a docker image to make it easy to run HiC-3DViwer.

To build the image, the easiest way it to use docker-compose as follow:

   git clone https://[email protected]/nadhir/hic3dviewer.git
   cd hic3dviewer/
   docker-compose build

When the image is built, you have two options, you can just go to the app directory and write

    docker-compose up

If your docker image is in another directory you can do

     docker-compose -f <destination_file/docker-compose.yml> up

The app should be running.

In your browser go to :

   localhost:5000

HiC-3DViewer should display.