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.
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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, an app store with an audience of millions.
Snap is available for Red Hat Enterprise Linux (RHEL) 8 and RHEL 7, from the 7.6 release onward.
The packages for RHEL 7, RHEL 8, and RHEL 9 are in each distribution’s respective Extra Packages for Enterprise Linux (EPEL) repository. The instructions for adding this repository diverge slightly between RHEL 7, RHEL 8 and RHEL 9, which is why they’re listed separately below.
The EPEL repository can be added to RHEL 9 with the following command:
sudo dnf install https://dl.fedoraproject.org/pub/epel/epel-release-latest-9.noarch.rpm
sudo dnf upgrade
The EPEL repository can be added to RHEL 8 with the following command:
sudo dnf install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm
sudo dnf upgrade
The EPEL repository can be added to RHEL 7 with the following command:
sudo rpm -ivh https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
Adding the optional and extras repositories is also recommended:
sudo subscription-manager repos --enable "rhel-*-optional-rpms" --enable "rhel-*-extras-rpms"
sudo yum update
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.
To install pathogenie, simply use the following command:
sudo snap install pathogenie --beta
Browse and find snaps from the convenience of your desktop using the snap store snap.
Interested to find out more about snaps? Want to publish your own application? Visit snapcraft.io now.