Objective: Goal is to set up local and server machines to run an ssh tunnel to enable anvio.

Protocol follows from anvio blog post here and here

Its a bit more complicated then in the blog post since in cologn I need to tunnel into a server machine and then tunnal from there.

On Server

• I created this file on the sever side to tell python how to connect to the web

cat << EOF > $(python -c "import os; print(os.path.join(os.path.dirname(os.path.abspath(os.__file__)), 'webbrowser.py'))")
def open_new(url):
    print("OPEN_ON_LOCAL[" + url + "]")

def register(*args, **kwargs):
    pass

def BackgroundBrowser(*args, **kwargs):
    pass
EOF

• Test if it worked:

python -c 'import webbrowser; print(webbrowser.__file__.rstrip("c"))'

This should print something like:

/path/to/anvio/env/lib/python3.6/webbrowser.py

To test of the module runs right:

python -c "import webbrowser; webbrowser.open_new('https://www.google.com/')"

This should print back:

OPEN_ON_LOCAL[https://www.google.com/]

-> Which is does successfully, we are on the right track!

• I needed to add a file to the following directory ~/miniconda3/envs/anvio-7/etc/conda/activate.d

File name: activate-interactive-ports.sh

#!/usr/bin/env bash
[[ "$(whoami)" = "sogin" ]] && export ANVIO_PORT=8100

Restart anvio and test if it worked:

echo $ANVIO_PORT

-> it worked

Locally

• I created an alias to logging into cologn and pasted it into my bash_profile or similar file (in this case .zshrc)

alias cologn="ssh -L 8100:localhost: 8100 sogin@your-uni-server | tee /dev/tty | python3 ~/.ssh/run_webbrowser.py"

Note: the number after the L must be the same as your port you enntered above in teh file activate-itneractive-ports.sh. You also need to modify the server address and alias name as needed

• I then needed to create the run_webbrowser.py file on my end in the .ssh folder:

~/.ssh/run_webbrowser.py

import sys
import webbrowser

for line in sys.stdin:
    if "OPEN_ON_LOCAL[" in line:
        line = line.replace("0.0.0.0", "127.0.0.1")
        webbrowser.open(line.split("OPEN_ON_LOCAL[")[1].split("]")[0])

• To log into cologn, just type cologn!
• Cologn requires one more additional step, run the tunnel again to a gc-node

ssh -L 8100:localhost:8100 gc-node-1

Tada!

note: if you want to log into an interactive session on the server you will need to do something extra that I’m not sure about yet.