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remove homebrew
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andrewjpage committed Jan 12, 2018
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Expand Up @@ -17,7 +17,6 @@ Theres are a number of dependancies required for Roary, with instructions specif
* CentOS/RedHat
* Bioconda - OSX/Linux
* Galaxy
* Homebrew/Linuxbrew - OSX/Linux
* Guix - Linux
* Virtual Machine - OSX/Linux/Windows
* Docker - OSX/Linux/Windows/Cloud
Expand All @@ -40,10 +39,7 @@ sudo cpanm -f Bio::Roary
```

### Ubuntu 12.04
Some of the software versions in apt are quite old so follow the instructions for [LinuxBrew](http://brew.sh/linuxbrew/) below.

## CentOS/RedHat
To install the dependancies, the easiest way is to install [LinuxBrew](http://brew.sh/linuxbrew/) using the steps for Fedora, then follow the steps below for installing Roary on LinuxBrew.
Some of the software versions in apt are quite old so follow the instructions for Bioconda below.

## Bioconda - OSX/Linux
Install conda. Then install bioconda and roary:
Expand All @@ -57,16 +53,7 @@ conda install roary
```

## Galaxy
Roary is available from the Galaxy toolshed ( as is Prokka).

## Homebrew/Linuxbrew - OSX/Linux
Assuming you have [homebrew](http://brew.sh/) (OSX) or [linuxbrew](http://brew.sh/linuxbrew/) (Linux) setup and installed on your system:

```
brew tap homebrew/science
brew install bedtools cd-hit blast mcl parallel prank mafft fasttree cpanm
sudo cpanm -f Bio::Roary
```
Roary is available from the Galaxy toolshed ( as is Prokka ).

## GNU Guix
Roary is included in [Guix](https://www.gnu.org/software/guix) and can be installed in the usual way:
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