Installing Anaconda on Mac OS X Anaconda is a package manager, an environment manager, and Python distribution that contains a collection of many open source packages. An installation of Anaconda comes with many packages such as numpy, scikit-learn, scipy, and pandas preinstalled and is also the recommended way to install Jupyter Notebooks. Getting started with conda¶ Conda is a powerful package manager and environment manager that you use with command line commands at the Anaconda Prompt for Windows, or in a terminal window for macOS or Linux. This 20-minute guide to getting started with conda lets you try out the major features of conda. MacOS Catalina was released on October 7, 2019, and has been causing quite a stir for Anaconda users. Apple has decided that Anaconda’s default install location in the root folder is not allowed. It moves that folder into a folder on your desktop called “Relocated Items,” in the Security folder.
Conda is an open source package management system and environmentmanagement system that runs on Windows, macOS and Linux. Condaquickly installs, runs and updates packages and their dependencies.Conda easily creates, saves, loads and switches between environmentson your local computer. It was created for Python programs, but itcan package and distribute software for any language.
Conda as a package manager helps you find and install packages.If you need a package that requires a different version ofPython, you do not need to switch to a different environmentmanager, because conda is also an environment manager. With justa few commands, you can set up a totally separate environment torun that different version of Python, while continuing to runyour usual version of Python in your normal environment.
In its default configuration, conda can install and manage thethousand packages at repo.anaconda.com that are built, reviewedand maintained by Anaconda®.
Conda can be combined with continuous integration systems suchas Travis CI and AppVeyor to provide frequent, automated testingof your code.
The conda package and environment manager is included in all versions ofAnaconda and Miniconda.
Conda is also included in Anaconda Enterprise, which provides on-site enterprisepackage and environment management for Python, R, Node.js, Java and otherapplication stacks. Conda is also available on conda-forge,a community channel. You may also get conda on PyPI,but that approach may not be as up to date.
Note:Bioconda supports only 64-bit Linux and Mac OS.
If you don’t want the hundreds of packages included with Anaconda, you can install Miniconda, a mini version of Anaconda that includes just conda, its dependencies, and Python. Tip Looking for Python 3.5 or 3.6? In this section you will download and install Miniconda, which will serve as the Python platform to access the Earth Engine API. As described above, you may use Miniconda or Anaconda, but to minimize impact to your system, this guide will describe a Miniconda installation with no alteration to your system's environmental variables. Install Python 3 using homebrew (brew install python) or by manually installing the package from Install python3 and python3-pip using the package manager of the Linux Distribution. Install conda using the Anaconda or miniconda installers or the miniforge installers (no administrator permission required for any of those). Install prerequisite packages; Install AFNI binaries; Install R; Setup Python (opt) Prepare for Bootcamp; Evaluate setup/system; Niceify terminal (optional, but goood) Install extras (optional, but recommended for Bootcamp prep) Keep up-to-date (remember!) 1.1.3. Linux, Ubuntu 16.04 - 17.10. Install prerequisite packages; Install. To run the silent installation of Miniconda for macOS or Linux, specify the -b and -p arguments of the bash installer. The following arguments are supported:-b-Batch mode with no PATH modifications to /.bashrc.
Bioconda requires the conda package manager to be installed. If youhave an Anaconda Python installation, you already have it. Otherwise,the best way to install it is with the
Minicondapackage. The Python 3 version is recommended.
On MacOS, run:
On Linux, run:
Follow the instructions in the installer. If you encounter problems,refer to the
Miniconda documentation. You can also join ourGitter channel to ask other users for help.
The conda FAQs explain howit’s easy to use with existing Python installations.
After installing conda you will need to add the bioconda channel as well as theother channels bioconda depends on. It is important to add them in thisorder so that the priority is set correctly (that is, conda-forge is highestpriority).
The conda-forge channel contains many general-purpose packages not alreadyfound in the
Browse the packages to see what’s available.
Bioconda is now enabled, so any packages on the bioconda channel can be installed into the current conda environment:
Or a new environment can be created:
We invite all parties interested in adding/editing package recipes to join the bioconda team,so that their pull requests don’t require merging by the core team or other members. To doso, please fork our recipes have a readthrough the Conda documentation.If you ping
@bioconda/core in a pull request we will review it and then add you to the team, if you desire.
Consider adding a badge to your posters and presentations to promotethat a tool can be easily installed from Bioconda.