More than 15 years ago I was working very hard on pplacer, a tool written in OCaml to analyze high-throughput DNA/RNA sequencing data in a phylogenetic context.
Since then I have moved research areas and pplacer has not been under active development.
The software works well still, and although it’s not the fastest program, it’s accurate and is viewed as a gold standard of sorts. People want to continue using it and are doing so using compiled binaries.
The difficulty is that it can’t be distributed using popular distribution mechanisms in biology such as conda-forge because it’s written for… OCaml 4.01.0.
We’d like to bring it up to OCaml 4.14, which is available for these platforms. But I see that OCaml 4 is EOL… so perhaps we can bring it up to 5?
I’m writing to ask if anyone would be willing to be our advisor in this upgrade. We are reasonably competent people, and code all the time, but I haven’t touched the OCaml toolchain in well over a decade so some help would be appreciated.
If you are interested, the current Dockerfile is available on the GH repo linked to above (as a new user I can’t directly link to it).
When I was working on pplacer the first time around, the OCaml community was just lovely and helpful, and I’ve always been grateful for that.
I wanted to say thanks for pplacer–I have used it some in the distant past, and always thought it was cool that it was in OCaml.
I’m interested in this too–I have had some reviewers ask me about putting software on conda-forge, but I have no experience getting OCaml programs on conda-forge.
It builds on OCaml 4.14 as well as on OCaml 5, which was the goal! It gives identical results in our tests so far.
Apparently I’m not able to post a GH link, but copying and pasting this will get you there:
github.com/matsen/pplacer/pull/386
Thank you to everyone, but especially to @nojb who did basically all of the work.
If anyone sees something that looks bad, let us know, otherwise we’ll merge and hopefully people will be able to use the same install method on conda-forge.
