Installation
Bactopia includes hundreds of tools in its workflow. As you can imagine installing these tools can turn into a very frustrating process. With this in mind, from the onset Bactopia was developed to only include programs that available from Bioconda and Conda-Forge.
(Optional) Install Conda via MambaForge¶
Conda is an open source package management system and environment management system that runs on Windows, Mac OSX, and Linux. By using packages available from Conda, we can streamline the installation process for the hundreds of tools that Bactopia uses.
If you do not have Conda installed I recommend installing MambaForge, as it comes with Mamba pre-installed. You'll want to follow the MambaForge Install Instructions for this. This will take a few minutes, but once complete you'll be ready to install Bactopia.
Installation¶
Once you have Conda all set up, you are ready to create an environment for Bactopia. To do so, you can use the following command:
mamba create -n bactopia -c conda-forge -c bioconda bactopia
After a few minutes you will have a new conda environment suitably named bactopia. To activate this environment, you will can use the following command:
conda activate bactopia
And voilà, you are all set to get started processing your data!
Windows and OSX Support¶
Windows is not supported, please use Windows Subsystem for Linux
Bactopia will never support Windows natively due to dependencies. To use Bactopia on a Windows machine, you will need to set up Windows Subsystem for Linux (WSL). This would allow you to run Bactopia inside the Linux subsystem. I have limited resources to test Bactopia in WSL, but if you give it a go and run into any issues please reach out!
OSX has limited support
I have developed Bactopia primarily for Linux, but I recognize it is useable on Mac OSX. Currently the support for OSX will be limited due to not having significant resources available for testing OSX extensively. Please keep this in mind when using Bactopia on OSX. I will still try to help out if you run into any issues!
Apple silicon (ARM) is not supported
Bactopia will not work on Apple silicon or other ARM processors. This is due to many of
the tools used by Bactopia not having an ARM compatible build. It is planned in Bioconda's
future, until then the best option is to use Docker to emulate linux/amd64 architecture.
This can be done by using the -profile arm option when running Bactopia.
Docker and Singularity¶
You can also use Bactopia with Docker or Singularity, but it is Nextflow that will be
handling this. This is done using the -profile option. For example, to use Docker you
would use -profile docker, and -profile singularity for Singularity.
When using these profiles, Nextflow will use Docker or Singularity for each process that
is executed. In other words, Nextflow will be using docker run or singularity exec
without the need for you to do anything else.
Always prefer containers over Conda
While I will be the first to admit that I love Conda, it is not perfect. Overtime tools can become broken or incompatible due to dependencies. Containers are a great way to avoid these issues. If you are using Bactopia, and have Docker or Singularity available I would recommend using them over Conda.
Run from GitHub Repository¶
Alternatively, if you already have Nextflow installed, and you don't want to use Conda to install Bactopia, you can run Bactopia directly from the GitHub repository.
nextflow run bactopia/bactopia
Missing out on helper commands
The Conda install of Bactopia comes with a few helper commands that are not available when running directly with Nextflow. These include commands to help prepare sample sheets, search public databases, pre-build environments, among other helper tools.