annotate README.rst @ 9:3bd420ec162d draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 7726c3cba165bdc8fc6366ec0ce6596e55657468
author galaxy-australia
date Tue, 13 Sep 2022 22:04:12 +0000
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children 81d1ef460bb3
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1 Alphafold compute setup
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2 =======================
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4 Overview
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5 --------
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7 Alphafold requires a customised compute environment to run. The machine
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8 needs a GPU, and access to a 2.2 Tb reference data store.
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10 This document is designed to provide details on the compute environment
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11 required for Alphafold operation, and the Galaxy job destination
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12 settings to run the wrapper. We strongly suggest reading this entire document
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13 to ensure that your setup is compatible with the hardware that you are
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14 deploying to.
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16 For full details on Alphafold requirements, see
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17 https://github.com/deepmind/alphafold.
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19 HARDWARE
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20 ~~~~~~~~
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22 The machine is recommended to have the following specs: - 12 cores - 80
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23 Gb RAM - 2.5 Tb storage - A fast Nvidia GPU.
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25 As a minimum, the Nvidia GPU must have 8Gb RAM. It also requires
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26 **unified memory** to be switched on. Unified memory is usually enabled
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27 by default, but some HPC systems will turn it off so the GPU can be
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28 shared between multiple jobs concurrently.
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30 ENVIRONMENT
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31 ~~~~~~~~~~~
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33 This wrapper runs Alphafold as a singularity container. The following
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34 software are needed:
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36 - `Singularity <https://sylabs.io/guides/3.0/user-guide/installation.html>`_
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37 - `NVIDIA Container
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38 Toolkit <https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html>`_
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40 As Alphafold uses an Nvidia GPU, the NVIDIA Container Toolkit is needed.
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41 This makes the GPU available inside the running singularity container.
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43 To check that everything has been set up correctly, run the following
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45 ::
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47 singularity run --nv docker://nvidia/cuda:11.0-base nvidia-smi
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49 If you can see something similar to this output (details depend on your
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50 GPU), it has been set up correctly.
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51
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52 ::
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54 +-----------------------------------------------------------------------------+
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55 | NVIDIA-SMI 470.57.02 Driver Version: 470.57.02 CUDA Version: 11.4 |
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56 |-------------------------------+----------------------+----------------------+
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57 | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
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58 | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
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59 | | | MIG M. |
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60 |===============================+======================+======================|
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61 | 0 Tesla T4 Off | 00000000:00:05.0 Off | 0 |
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62 | N/A 49C P0 28W / 70W | 0MiB / 15109MiB | 0% Default |
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63 | | | N/A |
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64 +-------------------------------+----------------------+----------------------+
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65
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66 +-----------------------------------------------------------------------------+
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67 | Processes: |
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68 | GPU GI CI PID Type Process name GPU Memory |
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69 | ID ID Usage |
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70 |=============================================================================|
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71 | No running processes found |
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72 +-----------------------------------------------------------------------------+
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73
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74 REFERENCE DATA
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75 ~~~~~~~~~~~~~~
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76
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77 Alphafold needs reference data to run. The wrapper expects this data to
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78 be present at ``/data/alphafold_databases``. A custom path will be read from
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79 the ALPHAFOLD_DB environment variable, if set. To download the AlphaFold,
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80 reference data, run the following shell script command in the tool directory.
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81
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82 ::
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83
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84 # make folders if needed
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85 mkdir /data /data/alphafold_databases
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86
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87 # download ref data
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88 bash scripts/download_all_data.sh /data/alphafold_databases
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89
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90 This will install the reference data to ``/data/alphafold_databases``.
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91 To check this has worked, ensure the final folder structure is as
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92 follows:
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93
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94 ::
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95
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96 data/alphafold_databases
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97 ├── bfd
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98 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
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99 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex
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100 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
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101 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex
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102 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
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103 │   └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
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104 ├── mgnify
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105 │   └── mgy_clusters_2018_12.fa
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106 ├── params
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107 │   ├── LICENSE
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108 │   ├── params_model_1.npz
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109 │   ├── params_model_1_ptm.npz
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110 │   ├── params_model_2.npz
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111 │   ├── params_model_2_ptm.npz
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112 │   ├── params_model_3.npz
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113 │   ├── params_model_3_ptm.npz
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114 │   ├── params_model_4.npz
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115 │   ├── params_model_4_ptm.npz
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116 │   ├── params_model_5.npz
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117 │   └── params_model_5_ptm.npz
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118 ├── pdb70
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119 │   ├── md5sum
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120 │   ├── pdb70_a3m.ffdata
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121 │   ├── pdb70_a3m.ffindex
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122 │   ├── pdb70_clu.tsv
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123 │   ├── pdb70_cs219.ffdata
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124 │   ├── pdb70_cs219.ffindex
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125 │   ├── pdb70_hhm.ffdata
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126 │   ├── pdb70_hhm.ffindex
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127 │   └── pdb_filter.dat
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128 ├── pdb_mmcif
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129 │   ├── mmcif_files
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130 │   └── obsolete.dat
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131 ├── uniclust30
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132 │   └── uniclust30_2018_08
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133 └── uniref90
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134 └── uniref90.fasta
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135
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136 JOB DESTINATION
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137 ~~~~~~~~~~~~~~~
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138
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139 Alphafold needs a custom singularity job destination to run. The
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140 destination needs to be configured for singularity, and some extra
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141 singularity params need to be set as seen below.
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142
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143 Specify the job runner. For example, a local runner
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144
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145 ::
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146
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147 <plugin id="alphafold_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
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148
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149 Customise the job destination with required singularity settings. The
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150 settings below are mandatory, but you may include other settings as
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151 needed.
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152
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153 ::
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154
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155 <destination id="alphafold" runner="alphafold_runner">
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156 <param id="dependency_resolution">'none'</param>
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157 <param id="singularity_enabled">true</param>
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158 <param id="singularity_run_extra_arguments">--nv</param>
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159 <param id="singularity_volumes">"$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/alphafold_databases:/data:ro"</param>
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160 </destination>
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161
7
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162 CUSTOM PARAMETERS
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163 ~~~~~~~~~~~~~~~~~
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164
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165 A few parameters can be customized with the use of environment variables set in the job destination:
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166
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167 - ``ALPHAFOLD_DB``: path to the reference database root (default ``/data``)
8
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168 - ``ALPHAFOLD_USE_GPU [True/False]``: set to ``False`` to disable GPU dependency (defaults to ``True``)
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169 - ``ALPHAFOLD_AA_LENGTH_MIN``: minimum accepted sequence length (default ``0``)
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170 - ``ALPHAFOLD_AA_LENGTH_MAX``: maximum accepted sequence length (default ``0`` - no validation)
7
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171
1
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172 Closing
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173 ~~~~~~~
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174
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175 If you are experiencing technical issues, feel free to write to
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176 help@genome.edu.au. We may be able to provide advice on setting up
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177 Alphafold on your compute environment.