--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Fri Jan 28 04:56:29 2022 +0000
@@ -0,0 +1,157 @@
+
+# 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.
+
+<br>
+
+### 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. <br>
+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.
+
+<br>
+
+### 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                                                 |
++-----------------------------------------------------------------------------+
+```
+
+
+<br>
+
+### REFERENCE DATA
+
+Alphafold needs reference data to run. The wrapper expects this data to be present at `/data/alphafold_databases`. <br>
+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
+```
+
+
+<br>
+
+### 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. <br>
+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>
+```
+
+<br>
+
+### Closing
+
+If you are experiencing technical issues, feel free to write to help@genome.edu.au. We may be able to provide comment on setting up Alphafold on your compute environment.