bfx-opam-repo

Opam repository to install bioinformatics tools (the non-OCaml ones).

Usage

If you got Opam with an OCaml compiler, these packages will work happily in the middle of any Opam switch:

opam remote add sm-bfx git@github.com:smondet/bfx-opam-repo
opam install samtools vcftools

If you got the binary version of Opam, without an OCaml compiler, and you don't want to compile OCaml, you can use the fake.0.0.1 “compiler”.

For instance, let's say you got Opam with apt-get install opam (with @avsm's PPA):

opam init --comp=fake.0.0.1 opamfake git@github.com:smondet/bfx-opam-repo
eval `opam config env`
opam install samtools vcftools

Notes

As a proof-of-concept there is a TMux package and its dependency: the library libevent; they work but require the following setup at runtime:

export LD_LIBRARY_PATH=`opam config var prefix`/lib:$LD_LIBRARY_PATH