Mercurial > repos > galaxy-australia > alphafold2
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"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
| author | galaxy-australia |
|---|---|
| date | Tue, 19 Apr 2022 00:39:29 +0000 |
| parents | abba603c6ef3 |
| children | ca90d17ff51b |
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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``. A custom path will be read from the ALPHAFOLD_DB environment variable, if set. To download the AlphaFold, reference data, 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> CUSTOM PARAMETERS ~~~~~~~~~~~~~~~~~ A few parameters can be customized with the use of environment variables set in the job destination: - ``ALPHAFOLD_DB``: path to the reference database root (default ``/data``) - ``ALPHAFOLD_AA_LENGTH_MIN``: minimum accepted sequence length (default ``30``) - ``ALPHAFOLD_AA_LENGTH_MAX``: maximum accepted sequence length (default ``2000``) For the last two, these could be set to ``0`` and ``50000`` respectively to remove the valiation entirely. 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.