README.rst

makebio

Manage computational biology projects with ease.

Installation

:code:pip install makebio

For autocompletion, add the following lines to your login file (BASH): :: eval "$(_MAKEBIO_COMPLETE=source makebio)"

Or for ZSH, :: eval "$(_MAKEBIO_COMPLETE=source_zsh makebio)"

Philosophy

:code:makebio is inspired by project management practices in :code:@theparkerlab and "A Quick Guide to Organizing Computational Biology Projects" by WS Noble [#]_. Using :code:makebio is easy and intuitive, and it is flexible enough to be used in a collaborative environment.

The core idea of :code:makebio is to create and manage a specific directory layout for your project. Using :code:makebio init, for example, will setup the following files and directories:

.. code-block:: project_dir/ bin/ control/ figures/ notebooks/ src/ results/ data/ --> symlink work/ --> symlink makebio.toml

This structure allows us to keep:

• analysis files in one place --- :code:control directory
• intermediate files in one place --- :code:work directory. You may symlink this directory to :code:/tmp, :code:/scratch space, or a destination with a large enough space.
• results (produced from workflows or scripts) in one place --- :code:results directory
• raw data in one place --- :code:data directory
• essential project files to reproduce your project results

Workflow ^^^^^^^^

#. Setup an empty project directory with :code:makebio init. #. Create a new analysis (:code:<NAME>) with :code:makebio add-analysis. This will create a (1) new directory in the :code:control/, and (2) a new directory in the :code:results/ directory with the name of the analysis. #. Add your analysis files in the :code:control/<NAME> directory. Make sure all the output is written to the :code:results/<NAME> directory. #. Save your project using :code:makebio save.

Usage

See :code:makebio --help.

.. code-block::

Usage: makebio [OPTIONS] COMMAND [ARGS]...

Manage computational biology research projects.

Computational biology or Bioinformatics projects utilize HPC systems that
typically limit the amount of space on your home directory and provide an
external mounted space for scratch work. The idea is that your code and
necessary files sit within the home directory and all intermediate files
which could take up a lot of space are kept on the scratch.

This necessitates organizing your work in such a way that even though the
underlying data is fragmented, it all should transparently appear in one
place for the user.

makebio is a simple utility to create and manage such projects. While
still in development, it is actively used by at least one person in their
daily bioinformatics work.

NOTES

`analysis` and `data` directories are prefixed with the date of creation.
For example, `2019-04-20_createTracks` or `2019-05-01_fastq`.

`freeze` marks the target directory and all files within to be read-only.

CONTACT

Please leave suggestions on and bugs reports on GitHub [1].

[1]: https://github.com/raivivek/makebio

@raivivek

Options: --version Show the version and exit. --help Show this message and exit.

Commands: add-analysis Add new analysis. add-data Add new data. freeze Mark a directory/file read only (for the user/group). init Initialize a new project. rename-analysis Rename existing analysis. save Save a (Git) snapshot. show Show current configuration. update Refresh configuration with new changes.

.. rubric:: Footnotes

.. [#] Noble W. S., 2009 A Quick Guide to Organizing Computational Biology Projects. PLOS Computational Biology 5: e1000424. https://doi.org/10.1371/journal.pcbi.1000424