<commit_before>---
layout: post
title: "Installing anvi'o"
excerpt: "Instructions to install the v2 branch of the platform."
modified: 2016-06-26 
tags: []
categories: [anvio]
redirect_from: /2015/05/01/installation/
comments: true
---

{% include _toc.html %}

{% include _project-anvio-version.html %}

This article explains basic steps of installing anvi'o using rather conventional methods.

Please post a comment down below if you have any questions about the installation. You may want to consider opening an <a href="https://github.com/meren/anvio/issues">issue</a> for more technical problems.

<div class="extra-info" markdown="1">

<span class="extra-info-header">A note on Chrome</span>

Currently, the [Chrome Web Browser](https://www.google.com/chrome/browser/desktop/) has the most efficient SVG engine among all browsers we tested. For instance, Safari can run the anvi'o interactive interface, however it takes orders of magnitude more time and memory compared to Chrome. Firefox, on the other hand, doesn't even bother drawing anything at all. Long story short, the anvi'o interactive interface __will not perform optimally__ with anything but Chrome. So you need Chrome. Moreover, if Chrome is not your default browser, every time interactive interface pops up, you will need to copy-paste the address bar into a Chrome window. You can learn what is your default browser by running this command in your terminal:

``` bash
python -c 'import webbrowser as w; w.open_new("http://")'
```

</div>

## Painless installation with Homebrew

If you are using Mac and have [Homebrew](http://brew.sh/) installed on your computer, all you need to do is to run this to have anvi'o installed on your system, and skip the rest of this page (although we suggest you to run `brew doctor` in your terminal first to make sure everything is good to go):

``` bash
brew install homebrew/science/anvio
```

If you are installing anvi'o on another operating system (or if you an OS X user who does not like Homebrew for some reason) please continue reading.


## Installation (with varying levels of pain)

First things first. You need to make sure your system does have all the following software if you are going to follow any of the following installation instructions. It is not as scary as it looks. If you just follow these links, you will most probably be golden:

* [samtools]({% post_url anvio/2016-06-18-installing-third-party-software %}#samtools){:target="_blank"}
* [Prodigal]({% post_url anvio/2016-06-18-installing-third-party-software %}#prodigal){:target="_blank"}
* [HMMER]({% post_url anvio/2016-06-18-installing-third-party-software %}#hmmer){:target="_blank"}
* [SQLite]({% post_url anvio/2016-06-18-installing-third-party-software %}#sqlite){:target="_blank"}
* [GSL]({% post_url anvio/2016-06-18-installing-third-party-software %}#gnu-scientific-library){:target="_blank"}
* [HDF5]({% post_url anvio/2016-06-18-installing-third-party-software %}#hdf5){:target="_blank"}

Finally you will need `virtualenv`. This should work for most:

``` bash
pip install virtualenv
```

{:.notice}<commit_msg><NAME> provides a conda package<commit_after>---
layout: post
title: "Installing anvi'o"
excerpt: "Instructions to install the v2 branch of the platform."
modified: 2016-06-26 
tags: []
categories: [anvio]
redirect_from: /2015/05/01/installation/
comments: true
---

{% include _toc.html %}

{% include _project-anvio-version.html %}

This article explains basic steps of installing anvi'o using rather conventional methods.

Please post a comment down below if you have any questions about the installation. You may want to consider opening an <a href="https://github.com/meren/anvio/issues">issue</a> for more technical problems.

<div class="extra-info" markdown="1">

<span class="extra-info-header">A note on Chrome</span>

Currently, the [Chrome Web Browser](https://www.google.com/chrome/browser/desktop/) has the most efficient SVG engine among all browsers we tested. For instance, Safari can run the anvi'o interactive interface, however it takes orders of magnitude more time and memory compared to Chrome. Firefox, on the other hand, doesn't even bother drawing anything at all. Long story short, the anvi'o interactive interface __will not perform optimally__ with anything but Chrome. So you need Chrome. Moreover, if Chrome is not your default browser, every time interactive interface pops up, you will need to copy-paste the address bar into a Chrome window. You can learn what is your default browser by running this command in your terminal:

``` bash
python -c 'import webbrowser as w; w.open_new("http://")'
```

</div>

## Painless installation with Homebrew

If you are using Mac and have [Homebrew](http://brew.sh/) installed on your computer, all you need to do is to run this to have anvi'o installed on your system, and skip the rest of this page (although we suggest you to run `brew doctor` in your terminal first to make sure everything is good to go):

``` bash
brew install homebrew/science/anvio
```

If you are installing anvi'o on another operating system (or if you an OS X user who does not like Homebrew for some reason) please continue reading.


## Painless installation with Conda

In case you have been working with [Anaconda](https://www.continuum.io/downloads) and would like to continue to so, there is a way to install anvi'o along with all Python and non-Python dependencies thanks to [<NAME>](https://scholar.google.com/citations?user=4S2q_9cAAAAJ&hl=en):

``` bash
conda create -n anvio232 -c bioconda -c conda-forge gsl anvio
```

Note that the most up-to-date conda-available anvi'o version, which is currently `v2.3.2`, may differ from the most up-to-date stable anvi'o version, which is `v{% include _project-anvio-version-number.html %}`.


## Installation (with varying levels of pain)

First things first. You need to make sure your system does have all the following software if you are going to follow any of the following installation instructions. It is not as scary as it looks. If you just follow these links, you will most probably be golden:

* [samtools]({% post_url anvio/2016-06-18-installing-third-party-software %}#samtools){:target="_blank"}
* [Prodigal]({% post_url anvio/2016-06-18-installing-third-party-software %}#prodigal){:target="_blank"}
* [HMMER]({% post_url anvio/2016-06-18-installing-third-party-software %}#hmmer){:target="_blank"}
* [SQLite]({% post_url anvio/2016-06-18-installing-third-party-software %}#sqlite){:target="_blank"}
* [GSL]({% post_url anvio/2016-06-18-installing-third-party-software %}#gnu-scientific-library){:target="_blank"}
* [HDF5]({% post_url anvio/2016-06-18-installing-third-party-software %}#hdf5){:target="_blank"}

Finally you will need `virtualenv`. This should work for most:

``` bash
pip install virtualenv
```

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