Conda (package manager)
Conda is an open-source, cross-platform, language-agnostic package manager and environment management system. It was originally developed to solve difficult package management challenges faced by Python data scientists, and today is a popular Python/R package manager. It is released under the Berkeley Software Distribution License by Anaconda Inc.
The big difference between conda and the pip package manager is in how package dependencies are managed, which is a significant challenge for Python data science and the reason conda was created. pip installs all Python package dependencies required, whether or not those conflict with other packages previously installed. So a working installation of, for example, Google TensorFlow can suddenly stop working when you pip-install a new package that needs a different version of the NumPy library. More insidiously, everything might still appear to work, but now you get different results, or you are unable to reproduce the same results elsewhere because you didn't pip-install in the same order.
Conda analyzes your current environment, everything you have installed, any version limitations you specify (e.g. you only want tensorflow >= 2.0) and figures out how to install compatible dependencies. Or it will tell you that what you want can't be done. pip, by contrast, will just install the package you specify and any dependencies, even if that breaks other packages.
Conda allows users to easily install different versions of binary software packages and any required libraries appropriate for their computing platform. Also, it allows users to switch between package versions and download and install updates from a software repository. Conda is written in the Python programming language, but can manage projects containing code written in any language (e.g., R), including multi-language projects. Conda can install the Python programming language, while similar Python-based cross-platform package managers (such as wheel or pip) cannot.
A popular conda channel for bioinformatics software is Bioconda, which provides multiple software distributions for computational biology. In fact, the conda package and environment manager is included in all versions of Anaconda, Miniconda, and Anaconda Repository.
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So now let’s say you need Python 3 to learn programming, but you don’t want to overwrite your Python 2.7 environment by updating Python. You can create and activate a new environment named snakes, and install the latest version of Python 3 as follows...
- Bioconda official website.
- Grüning, Bjorn; the Bioconda Team (27 October 2017). "Bioconda: A sustainable and comprehensive software distribution for the life sciences". bioRxiv 207092.
- "Miniconda". conda.io.
- "Anaconda repository". anaconda.org.
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