Installation
If you are new to our pipeline ecosystem, we recommend you first check out our general setup guide here.
Installing nextflow
Nextflow is a highly portable pipeline engine. Please see the official installation guide to learn how to set it up.
This pipeline expects Nextflow version 23.10.1, available here.
Software provisioning
This pipeline is set up to work with a range of software provisioning technologies - no need to manually install packages!
You can choose one of the following options:
The pipeline comes with simple pre-set profiles for all of these as described here; if you plan to use this pipeline regularly, consider adding your own custom profile to our central repository to better leverage your available resources. This will allow you to also use additional container/package managers not pre-configured in FooDMe2, as described here.
Installing the references
This pipeline requires locally stored references from Midori, UNITE and NCBI respectively. To build these, do:
Witha built-in profile:
nextflow run bio-raum/FooDMe2 -profile apptainer \\
--build_references \\
--run_name build_refs \\
--reference_base /path/to/references \\
-r <PIPELINE_VERSION>
where /path/to/references could be something like /data/pipelines/references or whatever is most appropriate on your system.
If you do not have apptainer on your system, you can also specify docker, singularity, podman or conda for software provisioning - see the usage information.
The path specified with --reference_base can then be given to the pipeline during normal execution as --reference_base (unless you already have set it as part of your site-specific config file).
Please note that the build process will create a pipeline-specific subfolder (foodme2) that must not be given as part of the --reference_base argument. FooDMe 2 is part of a collection of pipelines that use a shared reference directory and it will choose the appropriate subfolder by itself.
With a site-specific config file:
nextflow run bio-raum/FooDMe2 -profile your_profile \\
--build_references \\
--run_name build \\
-r <PIPELINE_VERSION>
Note that you do not have to specify --reference_base, as this option is pre-set in your profile.
IMPORTANT
In either case, this will download and format the various databases available through this pipeline. Please note that one of these databases is the full GenBank nt Eukaryote database, which has a final size of over 600GB (and growing), and will need over 1TB during installation. If your application works with single gene databases, you can skip installing this database with --skip_genbank.
nextflow run bio-raum/FooDMe2 -profile your_profile \\
--build_references \\
--run_name build \\
--skip_genbank \\
-r <PIPELINE_VERSION> \\
Site-specific config file
If you run on anything other than a local system, this pipeline requires a site-specific configuration file to be able to talk to your cluster or compute infrastructure. Nextflow supports a wide range of such infrastructures, including Slurm, LSF and SGE - but also Kubernetes and AWS. For more information, see here. In addition, a site-specific config file allows you to pre-set certain options specifically for your system and removes some of the complexity of the command line calls.
Site-specific config-files for our pipeline ecosystem are stored centrally on github. Please talk to us if you want to add your system.