Databases and Containers

Here are the locations on Viking where common databases or Apptainer containers are currently stored.

Note

Please contact us if you would like us to download any large data sets which other users can also benefit from. This can really help reduce duplicate data sets being downloaded and stored by multiple Viking users, taking up unnecessary space.

Databases

The folders containing databases or data sets on Viking can be found in the various sub folders within the projects directory:

/mnt/scratch/projects/

Attention

Some of the following paths can only be accessed after agreeing to a specific license, being part of a specific group or other similar limitations.

AlphaFold

AlphaFold2

The database directory for the previous version, AlphaFold2:

/mnt/scratch/projects/alphafold-db

AlphaFold3

The database and model directories for AlphaFold3:

• /mnt/scratch/projects/alphafold3-db

• /mnt/scratch/projects/alphafold3-model

Biology

/mnt/scratch/projects/biol-db/

The above folder contains the following sub folders for some common Biology data sets or databases:

• aMeta (https://github.com/NBISweden/aMeta)

• BLAST (https://blast.ncbi.nlm.nih.gov/)

• DRAM (https://github.com/WrightonLabCSU/DRAM/tree/dev)

• gt-db (https://gtdb.ecogenomic.org/)

• SpaceRanger (https://www.10xgenomics.com/support/software/space-ranger/downloads)

• Spectronaut (https://biognosys.com/software/spectronaut/)

Relion

The RELION database directory:

/mnt/scratch/projects/relion-db

Containers

A small selection of Apptainer containers are available when the usual software modules are not available, the location and currently available containers are:

/opt/apps/containers/

• AlphaFold-3

• BioEmu