Replace custom installation with opam or conda

[arahuja]

From @rleonid's work, a lot of tools custom installation can be replaced by a opam or conda invocation.

One tool, for example, is STAR. conda install star. I'd like to do this, but I'm not sure how conda.ml interfaces with the standard toolkit? Is there an example of a tool there installed by conda or opam?

[smondet]

To use all provided toolkits (custom-based and conda/opam-based), I have this:

    let toolkit =
      let default =
        Biokepi.Tool_providers.default_toolkit ()
          ~host ~meta_playground
          ~gatk_jar_location:(fun () -> gatk_jar_location)
          ~mutect_jar_location:(fun () -> mutect_jar_location) in
      let biopam =
        Biokepi.Biopam.default ()
          ~host ~install_path:(meta_playground // "biopam")
      in
      let mosaik = mosaik_binary_tool ~host ~meta_playground in
      Tool.Kit.{ tools = mosaik :: default.tools @ biopam.tools }  in

The order matters, so here above I put the default tools earlier than the biopam ones because custom installations are faster and more predictable, but you can do the other way around.

You can also add a tool in front of the list (like mosaik above) that installs the right STAR through Conda.