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.
On Arch Linux, snap can be installed from the Arch User Repository (AUR). The manual build process is the Arch-supported install method for AUR packages, and you’ll need the prerequisites installed before you can install any AUR package. You can then install snap with the following:
git clone https://aur.archlinux.org/snapd.git
cd snapd
makepkg -si
Once installed, the systemd unit that manages the main snap communication socket needs to be enabled:
sudo systemctl enable --now snapd.socket
If AppArmor is enabled in your system, enable the service which loads AppArmor profiles for snaps:
sudo systemctl enable --now snapd.apparmor.service
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.