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hammerlab / hlarp

Normalize HLA typing output.
Apache License 2.0
6 stars 1 forks source link

Add to biopam/bioconda #2

Closed ihodes closed 8 years ago

ihodes commented 8 years ago

Would be nice to use the biopam infrastructure in Biokepi to get this in!

rleonid commented 8 years ago

I am having second thoughts about biopam, in particular as a source for Biokepi tools. In particular:

  1. biopam doesn't have the volume of tools necessary to compete with other options (ex. bioconda).
  2. The tools that we do end up using are so flaky, so I am wary of investing more time in making them robust. It seems like it would be better to piggyback off of the efforts of other developers in larger communities (see previous point) to spread the load.
ihodes commented 8 years ago

That makes sense; are the problems you've seen with Bioconda unrelated to conda/related to how much of a pain it is to package some of these tools?

rleonid commented 8 years ago

The problems that I've experienced with bioconda in particular stem from trying to fight it. Conda follows the python development practice of resolving things when needed, so adding things to a PATH variable. Fighting against that by trying to find a specific library is onerous.

The packaging pain is just a constant factor worse than biopam; onerous documentation and more baroque fields to fill out. But on the plus side you can just add for a specific version of c++ to be installed too, if you have a weird dependency.

ihodes commented 8 years ago

In that case, is the recommended install path just regular opam?

rleonid commented 8 years ago

No, opam is better suited for projects in OCaml.

I am reticent to push tools that have such a unique utility into the public domain/repositories. My current preference would be bioconda, but for biokepi purposes I think we should maintain our own repo. Whether it should be opam or conda based is an open question; how many forks and of what projects does the lab want to maintain.

ihodes commented 8 years ago

Pushed to opam to get going on this for now.