---
title: Install pathogenie on CentOS using the Snap Store | Snapcraft
description: Get the latest version of pathogenie for on CentOS - microbial genome
  annotation and gene finding tool
url: https://snapcraft.io/install/pathogenie/centos
---

[Canonical Snapcraft](https://snapcraft.io/)

# Install pathogenie on **CentOS**

# pathogenie

[Damien Farrell (dmnfarrell)](https://snapcraft.io/publisher/dmnfarrell "View all snaps from Damien Farrell (dmnfarrell)")

* [Damien Farrell (dmnfarrell)](https://snapcraft.io/publisher/dmnfarrell "View all snaps from Damien Farrell (dmnfarrell)")
* [Science](https://snapcraft.io/search?categories=science)

[Install](https://snapcraft.io/install/pathogenie/centos#install)

#### microbial genome annotation and gene finding tool

pathogenie is a desktop and command line program for annotating draft bacterial
and viral genomes. It may also be used for quickly detecting arbitrary sequences such
as antibiotic resistance genes (AMR) proteins in nucleotide sequences. It uses Blast
to find hits to known gene sequences from sequence databases. The inputs are fasta files.
Annotation is performed in a similar manner to Prokka and first requires an assembled
genome if you have sequenced reads.
From the GUI you may load fasta files into a table and then run genome annotation or gene finding with custom databases. This program utilizes the sequence databases for gene finding compiled by abricate.
This program is under development. Suggestions are welcome.

### Package name

* pathogenie

---

### License

* GPL-3.0+

---

### Last updated

* 31 January 2021 - latest/beta

This snap hasn't been updated in a while. It might be unmaintained and have stability or security issues.

---

### Websites

* [github.com/dmnfarrell/pathogenie](https://github.com/dmnfarrell/pathogenie "https://github.com/dmnfarrell/pathogenie")

---

### Contact

* [github.com/dmnfarrell](https://github.com/dmnfarrell "https://github.com/dmnfarrell")

---

##### Report a Snap Store violation

* [Report this Snap](https://snapcraft.io/install/pathogenie/centos#report-snap-modal)

---

## Enable snaps on CentOS and install pathogenie

Snaps are applications packaged with all their dependencies to run on all popular Linux distributions from a single build. They update automatically and roll back gracefully.

Snaps are discoverable and installable from the [Snap Store](https://snapcraft.io/store), an app store with an audience of millions.

### Enable snapd

Snap is available for [CentOS 7.6+](https://snapcraft.io/install/pathogenie/centos), and Red Hat Enterprise Linux 7.6+, from the [Extra Packages for Enterprise Linux](https://fedoraproject.org/wiki/EPEL) (EPEL) repository. The EPEL repository can be added to your system with the following command:

```
sudo yum install epel-release
```

Snap can now be installed as follows:

```
sudo yum install snapd
```

Once installed, the *systemd* unit that manages the main snap communication socket needs to be enabled:

```
sudo systemctl enable --now snapd.socket
```

To enable *classic* snap support, enter the following to create a symbolic link between `/var/lib/snapd/snap` and `/snap`:

```
sudo ln -s /var/lib/snapd/snap /snap
```

Either log out and back in again, or restart your system, to ensure snap’s paths are updated correctly.

### Install pathogenie

To install pathogenie, simply use the following command:

```
sudo snap install pathogenie --beta
```

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