Higashi_vis set up

[BMDSKJ]

Hi Ruochi,

Thanks for developing the wonder tools: Higashi. I'm testing the visualization part with Higashi_vis.

As instructed, I first created directory below, . ├── Higashi │ ├── higashi │ └── config_dir └── └── visual_config.JSON

{ "config_list": [ {"path:/scHiC/Higashi/Ramani"}, ] }

Then I ran the bokeh connected command as instructed bokeh serve --port=$PORT1 --address=localhost --allow-websocket-origin=*:$PORT1 Higashi_vis/ ERROR: No 'main.py' or 'main.ipynb' in _path to /scHiC/Higashi/higashi/Higashivis

Did I miss something in this tutorial? What files should be in the Higashi_vis? Thank you.

[BMDSKJ]

By coping the higashi folder to the project folder, the ERROR message above was fixed However, with bokeh connection, there was a new error message.

When checking main.py under Higashi_vis folder, command line from 80 ~82 pasted below:

def get_config(config_path = "./config.jSON"):
        c = open(config_path,"r")
        return json.load(c)

I was not able to find config.jSON file anywhere in the Higashi folder. Is it normal ?

[BMDSKJ]

With Ruochi's quick and great help, the issue has been fixed. Thanks a lot, Ruochi! Below is the correct format for visual_config.JSON file: which without the 2nd pair {} mentioned in the document https://github.com/ma-compbio/Higashi/wiki/Higashi-vis-Usage#configure-the-higashi-vis

{
"config_list": [
"path:/scHiC/Higashi/Ramani"
]
}