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+Alphafold compute setup
+=======================
+
+Overview
+--------
+
+Alphafold requires a customised compute environment to run. The machine
+needs a GPU, and access to a 2.2 Tb reference data store.
+
+This document is designed to provide details on the compute environment
+required for Alphafold operation, and the Galaxy job destination
+settings to run the wrapper.
+
+For full details on Alphafold requirements, see
+https://github.com/deepmind/alphafold.
+
+HARDWARE
+~~~~~~~~
+
+The machine is recommended to have the following specs: - 12 cores - 80
+Gb RAM - 2.5 Tb storage - A fast Nvidia GPU.
+
+As a minimum, the Nvidia GPU must have 8Gb RAM. It also requires
+**unified memory** to be switched on. Unified memory is usually enabled
+by default, but some HPC systems will turn it off so the GPU can be
+shared between multiple jobs concurrently.
+
+ENVIRONMENT
+~~~~~~~~~~~
+
+This wrapper runs Alphafold as a singularity container. The following
+software are needed:
+
+-  `Singularity <https://sylabs.io/guides/3.0/user-guide/installation.html>`_
+-  `NVIDIA Container
+   Toolkit <https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html>`_
+
+As Alphafold uses an Nvidia GPU, the NVIDIA Container Toolkit is needed.
+This makes the GPU available inside the running singularity container.
+
+To check that everything has been set up correctly, run the following
+
+::
+
+   singularity run --nv docker://nvidia/cuda:11.0-base nvidia-smi
+
+If you can see something similar to this output (details depend on your
+GPU), it has been set up correctly.
+
+::
+
+   +-----------------------------------------------------------------------------+
+   | NVIDIA-SMI 470.57.02    Driver Version: 470.57.02    CUDA Version: 11.4     |
+   |-------------------------------+----------------------+----------------------+
+   | GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
+   | Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
+   |                               |                      |               MIG M. |
+   |===============================+======================+======================|
+   |   0  Tesla T4            Off  | 00000000:00:05.0 Off |                    0 |
+   | N/A   49C    P0    28W /  70W |      0MiB / 15109MiB |      0%      Default |
+   |                               |                      |                  N/A |
+   +-------------------------------+----------------------+----------------------+
+
+   +-----------------------------------------------------------------------------+
+   | Processes:                                                                  |
+   |  GPU   GI   CI        PID   Type   Process name                  GPU Memory |
+   |        ID   ID                                                   Usage      |
+   |=============================================================================|
+   |  No running processes found                                                 |
+   +-----------------------------------------------------------------------------+
+
+REFERENCE DATA
+~~~~~~~~~~~~~~
+
+Alphafold needs reference data to run. The wrapper expects this data to
+be present at ``/data/alphafold_databases``. To download, run the
+following shell script command in the tool directory.
+
+::
+
+   # make folders if needed
+   mkdir /data /data/alphafold_databases
+
+   # download ref data
+   bash scripts/download_all_data.sh /data/alphafold_databases
+
+This will install the reference data to ``/data/alphafold_databases``.
+To check this has worked, ensure the final folder structure is as
+follows:
+
+::
+
+   data/alphafold_databases
+   ├── bfd
+   │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
+   │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex
+   │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
+   │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex
+   │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
+   │   └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
+   ├── mgnify
+   │   └── mgy_clusters_2018_12.fa
+   ├── params
+   │   ├── LICENSE
+   │   ├── params_model_1.npz
+   │   ├── params_model_1_ptm.npz
+   │   ├── params_model_2.npz
+   │   ├── params_model_2_ptm.npz
+   │   ├── params_model_3.npz
+   │   ├── params_model_3_ptm.npz
+   │   ├── params_model_4.npz
+   │   ├── params_model_4_ptm.npz
+   │   ├── params_model_5.npz
+   │   └── params_model_5_ptm.npz
+   ├── pdb70
+   │   ├── md5sum
+   │   ├── pdb70_a3m.ffdata
+   │   ├── pdb70_a3m.ffindex
+   │   ├── pdb70_clu.tsv
+   │   ├── pdb70_cs219.ffdata
+   │   ├── pdb70_cs219.ffindex
+   │   ├── pdb70_hhm.ffdata
+   │   ├── pdb70_hhm.ffindex
+   │   └── pdb_filter.dat
+   ├── pdb_mmcif
+   │   ├── mmcif_files
+   │   └── obsolete.dat
+   ├── uniclust30
+   │   └── uniclust30_2018_08
+   └── uniref90
+       └── uniref90.fasta
+
+JOB DESTINATION
+~~~~~~~~~~~~~~~
+
+Alphafold needs a custom singularity job destination to run. The
+destination needs to be configured for singularity, and some extra
+singularity params need to be set as seen below.
+
+Specify the job runner. For example, a local runner
+
+::
+
+   <plugin id="alphafold_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
+
+Customise the job destination with required singularity settings. The
+settings below are mandatory, but you may include other settings as
+needed.
+
+::
+
+   <destination id="alphafold" runner="alphafold_runner">
+       <param id="dependency_resolution">'none'</param>
+       <param id="singularity_enabled">true</param>
+       <param id="singularity_run_extra_arguments">--nv</param>
+       <param id="singularity_volumes">"$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/alphafold_databases:/data:ro"</param>
+   </destination>
+
+Closing
+~~~~~~~
+
+If you are experiencing technical issues, feel free to write to
+help@genome.edu.au. We may be able to provide advice on setting up
+Alphafold on your compute environment.