Integrate ODGI as a submodule into the repository?

[subwaystation]

As the tool will heavily rely on ODGI, would it make sense to integrate it as a submodule into the repository?

[JervenBolleman]

I was hoping that we could have a conda/pip install of ODGI and have dependency management be done that way.

[subwaystation]

That sounds even better :)
I will knock on @ekg's door.

[ekg]

I don't know how to get the build for odgi to work within pip or conda. Would be happy to help but someone else with more experience should lead.

[subwaystation]

As far as I know, a pure C++ project like odgi won't work on pip but we can bring it to conda, of course.
I will ask @apeltzer how we do that.

[subwaystation]

@JervenBolleman I am not sure, what the plan will be. Do we just want be able to install odgi via conda and integrate it via a command line call?
Or do we talk to odgi via the python bindings @ekg created?

[JervenBolleman]

We definitely want to continue with the python bindings that @ekg did. At scale the cost of reloading the same graph from disk over and over will be to high with cli. So me also not being the python hero, would like to see a way that conda can put the C++/python module lib directly on the python path.

Basically it should be as standard as possible so a conda install away would be best.
Then we can have requirements.txt. that just asks for a odgi module.

[subwaystation]

I have to admit I never ran into the case where one wants to make a C++/Python module library available on Conda. But I will ask some people who might have.

[JervenBolleman]

I was thinking of pytorch as the canonical example of having C/C++ in conda.

[apeltzer]

Jumping right in here and having added quite some tools to Bioconda / conda-forge recently:

It will be definitely possible to have both odgi and the spodgi tool(s) in bioconda as they both work on genome graphs which is a (computational) biology domain so to say.

I can help in getting this done, but ideally, there should be a release of both projects on Github first, that one can refer to directly with a URL (see here on how to do that).

Once this is done, @subwaystation and I can take care of the bioconda recipes for both odgi and spodgi. Also, if you need more recipes within the project(s) here, let me know and I can help on that. Planning to use your stuff at some point, so getting in touch sounds like a win-win for everyone here :-)

[subwaystation]

@JervenBolleman If you have time, you can take a look at pangenome/odgi#75 (comment).