<commit_before>---
layout: post
title: "Installing third-party software"
excerpt: "Recipes to install various software tools anvi'o uses"
modified: 2016-06-18
categories: [anvio]
comments: true
---

This article describes some recipes to install software written by other groups.

Most software we rely on to enhance anvi'o's abilities *do* allow us to re-distribute their code, or have them pre-installed, however, we do not want to follow that route. Although doing that would have made your life much easier, internalizing third-party software from within other platforms directly makes users unable to appreciate other groups' efforts.

As an apology, we will do our best to keep this article up-to-date, so installing third-party software anvi'o uses will not be a big hassle for you. Thank you for your understanding, and your patience in advance.

{% include _toc.html %}

## Prodigal

[Prodigal](http://prodigal.ornl.gov/) is a bacterial and archaeal gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Everytime you create a contigs database in anvi'o with `anvi-gen-profile-database`, you use it.

**Citation**: [http://www.biomedcentral.com/1471-2105/11/119](http://www.biomedcentral.com/1471-2105/11/119)

Go to your terminal, and type `prodigal -v` if you get an error, you need to install it, __if the version number is smaller than 2.6.2__, you need to update it.

Here is how to install v2.6.2 (the first line will not work if you don't have wget, but you can get wget installed esily typing `sudo port install wget` if you are using MacPorts system on your Mac computer):

{% highlight bash %}
wget https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz
tar -zxvf v2.6.2.tar.gz && cd Prodigal-2.6.2/ && make
sudo cp prodigal /usr/bin/
{% endhighlight %}

Type `prodigal -v` again to make sure everything is alright, and you get the proper version number.

## HMMER

[HMMER](http://hmmer.org/) uses hidden Markov models to perform sequence search and alignments. Everytime you run `anvi-run-hmmss` program, you use it.

**Citation**: [http://hmmer.org/](http://hmmer.org/)

Go to your terminal, adn type `hmmscan -h`, if you get an error, you need to install HMMER, if the version number is less than 3.1, you ned to update it.

Here is how to install v3.1b2:

{% highlight bash %}<commit_msg>better to copy here<commit_after>---
layout: post
title: "Installing third-party software"
excerpt: "Recipes to install various software tools anvi'o uses"
modified: 2016-06-18
categories: [anvio]
comments: true
---

This article describes some recipes to install software written by other groups.

Most software we rely on to enhance anvi'o's abilities *do* allow us to re-distribute their code, or have them pre-installed, however, we do not want to follow that route. Although doing that would have made your life much easier, internalizing third-party software from within other platforms directly makes users unable to appreciate other groups' efforts.

As an apology, we will do our best to keep this article up-to-date, so installing third-party software anvi'o uses will not be a big hassle for you. Thank you for your understanding, and your patience in advance.

{% include _toc.html %}

## Prodigal

[Prodigal](http://prodigal.ornl.gov/) is a bacterial and archaeal gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Everytime you create a contigs database in anvi'o with `anvi-gen-profile-database`, you use it.

**Citation**: [http://www.biomedcentral.com/1471-2105/11/119](http://www.biomedcentral.com/1471-2105/11/119)

Go to your terminal, and type `prodigal -v` if you get an error, you need to install it, __if the version number is smaller than 2.6.2__, you need to update it.

Here is how to install v2.6.2 (the first line will not work if you don't have wget, but you can get wget installed esily typing `sudo port install wget` if you are using MacPorts system on your Mac computer):

{% highlight bash %}
wget https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz
tar -zxvf v2.6.2.tar.gz && cd Prodigal-2.6.2/ && make
sudo cp prodigal /usr/local/bin/
{% endhighlight %}

Type `prodigal -v` again to make sure everything is alright, and you get the proper version number.

## HMMER

[HMMER](http://hmmer.org/) uses hidden Markov models to perform sequence search and alignments. Everytime you run `anvi-run-hmmss` program, you use it.

**Citation**: [http://hmmer.org/](http://hmmer.org/)

Go to your terminal, adn type `hmmscan -h`, if you get an error, you need to install HMMER, if the version number is less than 3.1, you ned to update it.

Here is how to install v3.1b2:

{% highlight bash %}
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