Overview

• Installation
  • Docker
    • Docker build
    • Building arguments
  • Linux
• Configuration
• Three-Layer-Design
  • Web-Interface
  • Accumulator
• Extension
  • Extension example for CpG islands annotation
  • Extension example for barrnap rRNA annotation
  • Extension example for replacing muscle with kalign
• Frequently Ask Questions (FAQ)

Installation

Requirements

• 60-80 GB free disk space
• 16 GB ram
• Linux/Windows on a x64 platform for Docker
• We recommend to use at least 8 CPU cores

Docker

Easiest way to install the pipeline is to use our last released Docker image:

docker pull registry.gitlab.com/mosga/mosga:latest
docker run --publish 8000:80 --detach --name mosga registry.gitlab.com/mosga/mosga:latest

You can open the pipeline by opening a web browser and type in http://localhost:8000 as the address. If you run the docker container you have to use the IP address or hostname instead localhost.

The first run will cause the download of the EggNog 5, SILVA and Swiss-Prot database. In total it requires ~60 GB disk space. Please be patient, since MOSGA will only starts after the downloads are finnished. The database downloads are skipped by our builds due to the huge image size.

Docker Build

To build your own Docker image you should download this repository and run the docker build command.

git clone --depth 1 https://gitlab.com/mosga/mosga.git
cd mosga
sudo docker build ./ 

There are some build arguments that can be applied. Check them out here.

BRAKER/GeneMark

You can build your image including BRAKER with GeneMark. Since GeneMark is not freely accessible to download you have to download the Linux GeneMark on your own and store the gmes_linux_64.tar.gz file into this repository. The docker build will recognize this file and activate the BRAKER prediction tools.

Linux

We do not recommend to install the pipeline on an already existing Linux system, but it is possible to run it in a virtual machine without any issues. Just follow the following installation guide.