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, :doc:`AlphaFold2 <../applications/alphafold>`: ``/mnt/scratch/projects/alphafold-db`` AlphaFold3 """""""""" The database and model directories for :doc:`AlphaFold3 <../applications/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 :doc:`Apptainer <../applications/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