OPAM repository for bioinformatics tools

Biopam provides the ability to install many bioinformatics packages with relative ease. For example, to install samtools, you need only type opam install samtools. Packages' source code are automatically downloaded, and their libraries, executables, and documentation are automatically built and installed. Everything goes under the single directory ~/.opam, which you can delete to remove all effects of using biopam if desired. This work makes use of the excellent OPAM package manager, which is widely used for packages in other domains also.

The rest of this documentation is targeted at 3 audiences:

1. Users - Data analysts in the field of biology who wish to use various bioinformatics tools. The subsequent section provides all the information you need to make effective use of Biopam. You can largely ignore all other content of this repo.

2. Package Developers - If biopam doesn't have a package you need, you can submit a pull request to add one. In this case, you will need to understand how a package is specified. The packages/ directory of this repo is largely what is relevant to you.

3. Tool Developers - Some code is available to test packages and help package developers. This code is implemented in the bin/ directory.

Users

Biopam makes use of the opam tool, so you must first install that. The quickest way is to grab one of their binary releases. Download the binary corresponding to your architecture, put it somewhere in your PATH, and rename the executable to opam (if you don't understand these instructions, please ask a colleague comfortable with Unix for assistance). For other options, see the full installation instructions here.

Once you have opam installed, you need to initialize it and tell it to look for the package descriptions provided by biopam by doing:

opam init -n --compiler=0.0.0 biopam https://github.com/solvuu/biopam.git

That's it. Now you can start installing packages, e.g.

opam install bwa samtools picard

Run opam --help for more commands and options. Some immediately useful ones are:

• opam list -a to print a list of all available packages.

• opam info <pkg> to see information about a particular package, replace <pkg> with the actual name of a package.

• opam install <pkg>.<version> to install a specific version of a package. For example, opam install samtools.0.1.19 will install that version even though more recent versions are available.

• opam switch -A 0.0.0 <my-project> to create an installation for a specific project with a name of your choice. Now you can install particular versions of various tools as needed for this project. Create another switch for another project, and you can cleanly maintain different sets of tools for different projects.

Package Developers

See packaging instructions on OPAM's site, and submit pull requests.

Python scripts

It is (lightly) suggested that Python scripts be converted to standalone executables via Pyinstaller. This clarifies what version of Python is required by the script (2.7 or 3.5). It also resolves all of the scripts library dependencies (eg. numpy, biopython) so that the user can make sure they are installed before running the application. This is readily accomplished via Pyinstaller-spec file, OptiType provides a good example.

Tool Developers

See code under the bin/ directory.

License

We follow the main OPAM repository, and release all metadata contained in this repository under the CC0 1.0 Universal license. Please understand this license regards only the descriptions of packages as provided in this repo. The licenses of the tools that biopam lets you install is of course dictated by their respective authors.