https://github.com/smondet/bfx-opam-repo

Opam repository to install bioinformatics tools (non-OCaml)
https://github.com/smondet/bfx-opam-repo

Last synced: 16 days ago
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Opam repository to install bioinformatics tools (non-OCaml)

• Host: GitHub
• URL: https://github.com/smondet/bfx-opam-repo
• Owner: smondet
• Created: 2014-08-07T18:38:32.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2014-08-15T18:05:50.000Z (over 10 years ago)
• Last Synced: 2023-03-12T03:03:27.897Z (almost 2 years ago)
• Size: 161 KB
• Stars: 2
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
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 [email protected]: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](https://launchpad.net/~avsm/+archive/ubuntu/ppa)):

    opam init --comp=fake.0.0.1 opamfake [email protected]: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