Genscale Team edited this page Jun 9, 2017 · 15 revisions

Presentation

pyGATB is a Python3 wrapper for the GATB-Core library.

The current release of pyGATB gives access to the following GATB-Core components:

  • Bank: the class that enables to load a Fasta or a Fastaq file
  • Graph: the class that holds the De Bruijn graph
  • Node: the class that makes graph's nodes

Learn more.

Requirements and installation

Actually, pyGATB requirements depend upon the way you use the wrapper:

  • You can execute pyGATB Python scripts using a Docker container
  • You could also install pyGATB pre-compiled Python3 library
  • Finally, you may want to compile pyGATB code on your system

Each solution has its pros and cons. Let's have a review of that.

Use pyGATB with Docker

Using the Docker option is quite easy.

  • Pros:
    • it only requires you have Docker installed on your system
      you do not even need to have Python3 installed.
  • Cons:
    • Docker has to be installed
    • you have limited access to the full power of your computer (e.g. cores usage)

It is a perfect solution if you just want to make a try of pyGATB.

Read more.

Use pyGATB Python3 package

If you want to get a bit further in taking advantage of your computer resources, you can install a pre-compiled pyGATB package.

  • Pros: pyGATB is simply installed using Python3 standard installation package
  • Cons:
    • Python3 has to be installed
    • pyGATB package requires recent libc++

Read more.

Use pyGATB from its source code

Finally, the most extended way of using pyGATB relies on making an installation from the source code.

  • Pros: benefit from a precise use of the full architecture of YOUR computer.
  • Cons: you have to install the pyGATB compiling stack

Read more.

GATB-Core to Python: How does it work?

You can read this article to understand how Cython is used to provide native GATB-Core c++ APIs to the Python programming language.

You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.