How to run image once built

[mmingay2]

Thanks for creating this. I am trying to build the image and run it.

python test.py works well so I build the image with docker build -t igvtest3 ./context and it builds fine.

Then I try to run it with docker run --rm -p 8080:8080 igvtest3:latest and it hangs for a while then I ctrl+c and get an error related to the SocketServer.py. Error looks like this:

File "on_startup.py", line 95, in
start_server()
File "on_startup.py", line 82, in start_server
SocketServer.TCPServer(("", 80), Handler).serve_forever()
File "/usr/local/lib/python2.7/SocketServer.py", line 231, in serve_forever
poll_interval)
File "/usr/local/lib/python2.7/SocketServer.py", line 150, in _eintr_retry
return func(*args)
KeyboardInterrupt

any suggestions?

thanks,

Matt

[mccalluc]

@mmingay2 : Sorry to miss this. I'll look at it latter today and try to say something useful. Thanks!

[scottx611x]

@mmingay2 Sorry for missing this as well.

The following should get you a local instance running at http://localhost:8080

docker run -p 8080:80 -e INPUT_JSON_URL=https://raw.githubusercontent.com/refinery-platform/docker_igv_js/master/input_fixtures/good/input.json docker_igv_js

The caveat here being that we are providing input files to the conatiner in a very specific means based off of a JSONSchema in our parent project: refinery-platform. We are providing said input data through a JSON file either from a url (INPUT_JSON_URL, as I've done in the example above) or within an env var passed directly to the container (INPUT_JSON).

Our input format may be overkill for your needs so I see two paths if you are still interested in utilizing what we have:

• Construct your own INPUT_JSON and provide it to the container as an envvar

  • docker run -p 8080:80 -e INPUT_JSON='
      {
        "node_info": {
          "id-1": {
            "file_url": "https://raw.githubusercontent.com/igvteam/igv/master/test/data/bed/intervalTest.bed",
            "node_solr_info": {"name": "track-name"}
          }
        },
        "parameters": [
          {"name": "Genome Build", "value": "hg19"}
        ]
      }' gehlenborglab/docker_igv_js
    

• Or fork this repo and take a stab at editing get_refinery_input() & write_igv_configuration() as needed. If you choose this path we'll be more than happy to help.

Again, apologies that we hadn't envisioned this as a more general-purpose solution!

---

EDIT: I've since updated the README