conda and bioconda channel

Anaconda ( https://www.continuum.io/downloads ) provides a Python distribution with more than 400 of the most popular Python packages for science, math, engineering, and data analysis. Anaconda installs an executable called conda that will be your entry point.

Anaconda solves two problems.

First it is a virtual environment similar to virtualenv, which is used in the Python community. The advantage I found with compared to a tool such as virtualenv is that you can easily have any Python environment on your system (e.g. 2.6, 3.4 and so on) without the need to have to install the specific Python version yourself (see other posts on this subjet , , .

Second, installation of packages (e.g. numpy) to be found on the conda website will be fast and smooth since packages are pre-compiled: no compilation errors (in principle) and no time spent waiting for the compilation to be finished. This is very valuable since it also means that your software can be installed by anybody who will use anaconda (and therefore the same pre-compiled libraries as yours).

conda can download more than 400 packages but there are much more out there ! First, you can still use pip to install any package to be found on website.
Besides, conda provides a mechanism that ease the creation of parallel channels. One of them dedicated to biology is called bioconda. The bioconda channel can be added to your environment by typing

You can then install a tool such as bwa (sequence alignment) as follows:

Again the great advantages here will be that bwa will be installed in a second (time to download the package) and the executable ready to be used !

I mentionned the fact that you can use different version of Python. How does that work ? You need to create an environment. A default one is provided once Anaconda is installed but you can create as many as you want by naming them and setting the version of Python to be used. For instance, let us create an environment with python3.5:

You can then activate it as follows:

You can check that you have indeed the correct python version by starting a python shell and check the version

For more information, visit those two sites:

https://bioconda.github.io/
https://www.continuum.io/downloads

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One Response to conda and bioconda channel

  1. peter says:

    Thank you Thomas.

    Conda seems like a really handy Python distribution. I will test it.

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