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annotate README.rst @ 14:d00e15139065 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au commit d490defa32d9c318137d2d781243b392cb14110d-dirty
author galaxy-australia
date Tue, 28 Feb 2023 01:15:42 +0000
parents 7fbec959cf2b
children f9eb041c518c
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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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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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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.
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81 To download the AlphaFold reference DBs:
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83 ::
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84
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85 # Set your AlphaFold DB path
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86 ALPHAFOLD_DB=/data/alphafold_databases
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88 # Set your target AlphaFold version
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89 ALPHAFOLD_VERSION= # e.g. 2.1.2
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91 # Download repo
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92 wget https://github.com/deepmind/alphafold/releases/tag/v${ALPHAFOLD_VERSION}.tar.gz
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93 tar xzf v${ALPHAFOLD_VERSION}.tar.gz
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94
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95 # Ensure dirs
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96 mkdir -p $ALPHAFOLD_DB
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97
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98 # Download
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99 bash alphafold*/scripts/download_all_data.sh $ALPHAFOLD_DB
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100
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101 You will most likely want to run this as a background job, as it will take a
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102 very long time (7+ days in Australia).
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103
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104 This will install the reference data to your ``$ALPHAFOLD_DB``.
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105 To check this has worked, ensure the final folder structure is as
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106 follows:
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107
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108 ::
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109
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110 # NOTE: this structure will change between minor AlphaFold versions
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111 # The tree shown below was updated for v2.3.1
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112
1
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113 data/alphafold_databases
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114 ├── bfd
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115 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
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116 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex
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117 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
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118 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex
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119 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
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120 │   └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
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121 ├── mgnify
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122 │   └── mgy_clusters_2022_05.fa
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123 ├── params
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124 │   ├── LICENSE
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125 │   ├── params_model_1.npz
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126 │   ├── params_model_1_multimer_v3.npz
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127 │   ├── params_model_1_ptm.npz
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128 │   ├── params_model_2.npz
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129 │   ├── params_model_2_multimer_v3.npz
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130 │   ├── params_model_2_ptm.npz
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131 │   ├── params_model_3.npz
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132 │   ├── params_model_3_multimer_v3.npz
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133 │   ├── params_model_3_ptm.npz
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134 │   ├── params_model_4.npz
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135 │   ├── params_model_4_multimer_v3.npz
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136 │   ├── params_model_4_ptm.npz
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137 │   ├── params_model_5.npz
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138 │   ├── params_model_5_multimer_v3.npz
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139 │   └── params_model_5_ptm.npz
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140 ├── pdb70
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141 │   ├── md5sum
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142 │   ├── pdb70_a3m.ffdata
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143 │   ├── pdb70_a3m.ffindex
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144 │   ├── pdb70_clu.tsv
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145 │   ├── pdb70_cs219.ffdata
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146 │   ├── pdb70_cs219.ffindex
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147 │   ├── pdb70_hhm.ffdata
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148 │   ├── pdb70_hhm.ffindex
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149 │   └── pdb_filter.dat
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150 ├── pdb_mmcif
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151 │   ├── mmcif_files
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152 │   └── obsolete.dat
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153 ├── pdb_seqres
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154 │   └── pdb_seqres.txt
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155 ├── uniprot
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156 │   └── uniprot.fasta
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157 ├── uniref30
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158 │   ├── UniRef30_2021_03.md5sums
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159 │   ├── UniRef30_2021_03_a3m.ffdata
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160 │   ├── UniRef30_2021_03_a3m.ffindex
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161 │   ├── UniRef30_2021_03_cs219.ffdata
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162 │   ├── UniRef30_2021_03_cs219.ffindex
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163 │   ├── UniRef30_2021_03_hhm.ffdata
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164 │   └── UniRef30_2021_03_hhm.ffindex
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165 └── uniref90
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166 └── uniref90.fasta
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167
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168 In more recent releases of the AlphaFold tool, you will need to download an
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169 additional file to allow the ``reduced_dbs`` option:
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170
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171 ::
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172
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173 bash scripts/download_small_bfd.sh $ALPHAFOLD_DB_ROOT
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174
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175 The ``$ALPHAFOLD_DB_ROOT`` directory should now contain this additional file:
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176
12
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177 ::
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178
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179 data/alphafold_databases
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180 ├── small_bfd
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181 │   └── bfd-first_non_consensus_sequences.fasta
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182
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183
14
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184 **Upgrading database versions**
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185
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186 When upgrading to a new minor version of AlphaFold, you will most likely have to
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187 upgrade the reference database. This can be a pain, due to the size of the
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188 databases and the obscurity around what has changed. The simplest way to do
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189 this is simply create a new directory and download the DBs from scratch.
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190 However, you can save a considerable amount of time by downloading only the
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191 components that have changed.
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192
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193 If you wish to continue hosting prior versions of the tool, you must maintain
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194 the reference DBs for each version. The ``ALPHAFOLD_DB`` environment variable
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195 must then be set respectively for each tool version in your job conf (on Galaxy
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196 AU this is currently `configured with TPV<https://github.com/usegalaxy-au/infrastructure/blob/master/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml#L1515-L1554>`_).
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197
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198 To minimize redundancy between DB version, we have symlinked the database
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199 components that are unchanging between versions. In ``v2.1.2 -> v2.3.1`` the BFD
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200 database is the only component that is persistent, but they are by far the
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201 largest on disk.
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202
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203
1
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204 JOB DESTINATION
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205 ~~~~~~~~~~~~~~~
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206
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207 Alphafold needs a custom singularity job destination to run. The
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208 destination needs to be configured for singularity, and some extra
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209 singularity params need to be set as seen below.
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210
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211 Specify the job runner. For example, a local runner
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212
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213 ::
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214
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215 <plugin id="alphafold_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
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216
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217 Customise the job destination with required singularity settings. The
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218 settings below are mandatory, but you may include other settings as
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219 needed.
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220
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221 ::
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222
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223 <destination id="alphafold" runner="alphafold_runner">
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224 <param id="dependency_resolution">'none'</param>
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225 <param id="singularity_enabled">true</param>
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226 <param id="singularity_run_extra_arguments">--nv</param>
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227 <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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228 </destination>
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229
7
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230 CUSTOM PARAMETERS
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231 ~~~~~~~~~~~~~~~~~
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232
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233 A few parameters can be customized with the use of environment variables set in the job destination:
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234
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235 - ``ALPHAFOLD_DB``: path to the reference database root (default ``/data``)
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236 - ``ALPHAFOLD_USE_GPU [True/False]``: set to ``False`` to disable GPU dependency (defaults to ``True``)
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237 - ``ALPHAFOLD_AA_LENGTH_MIN``: minimum accepted sequence length (default ``0``)
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238 - ``ALPHAFOLD_AA_LENGTH_MAX``: maximum accepted sequence length (default ``0`` - no validation)
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239
1
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240 Closing
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241 ~~~~~~~
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242
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243 If you are experiencing technical issues, feel free to write to
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244 help@genome.edu.au. We may be able to provide advice on setting up
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245 Alphafold on your compute environment.