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annotate README.rst @ 1:6c92e000d684 draft

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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit a510e97ebd604a5e30b1f16e5031f62074f23e86"
author galaxy-australia
date Tue, 01 Mar 2022 02:53:05 +0000
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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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9
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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.
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14 For full details on Alphafold requirements, see
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15 https://github.com/deepmind/alphafold.
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17 HARDWARE
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18 ~~~~~~~~
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20 The machine is recommended to have the following specs: - 12 cores - 80
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21 Gb RAM - 2.5 Tb storage - A fast Nvidia GPU.
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23 As a minimum, the Nvidia GPU must have 8Gb RAM. It also requires
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24 **unified memory** to be switched on. Unified memory is usually enabled
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25 by default, but some HPC systems will turn it off so the GPU can be
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26 shared between multiple jobs concurrently.
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28 ENVIRONMENT
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29 ~~~~~~~~~~~
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31 This wrapper runs Alphafold as a singularity container. The following
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32 software are needed:
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34 - `Singularity <https://sylabs.io/guides/3.0/user-guide/installation.html>`_
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35 - `NVIDIA Container
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36 Toolkit <https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html>`_
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38 As Alphafold uses an Nvidia GPU, the NVIDIA Container Toolkit is needed.
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39 This makes the GPU available inside the running singularity container.
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41 To check that everything has been set up correctly, run the following
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43 ::
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45 singularity run --nv docker://nvidia/cuda:11.0-base nvidia-smi
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47 If you can see something similar to this output (details depend on your
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48 GPU), it has been set up correctly.
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49
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50 ::
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52 +-----------------------------------------------------------------------------+
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53 | NVIDIA-SMI 470.57.02 Driver Version: 470.57.02 CUDA Version: 11.4 |
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54 |-------------------------------+----------------------+----------------------+
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55 | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
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56 | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
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57 | | | MIG M. |
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58 |===============================+======================+======================|
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59 | 0 Tesla T4 Off | 00000000:00:05.0 Off | 0 |
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60 | N/A 49C P0 28W / 70W | 0MiB / 15109MiB | 0% Default |
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61 | | | N/A |
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62 +-------------------------------+----------------------+----------------------+
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63
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64 +-----------------------------------------------------------------------------+
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65 | Processes: |
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66 | GPU GI CI PID Type Process name GPU Memory |
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67 | ID ID Usage |
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68 |=============================================================================|
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69 | No running processes found |
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70 +-----------------------------------------------------------------------------+
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71
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72 REFERENCE DATA
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73 ~~~~~~~~~~~~~~
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75 Alphafold needs reference data to run. The wrapper expects this data to
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76 be present at ``/data/alphafold_databases``. To download, run the
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77 following shell script command in the tool directory.
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79 ::
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81 # make folders if needed
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82 mkdir /data /data/alphafold_databases
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84 # download ref data
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85 bash scripts/download_all_data.sh /data/alphafold_databases
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86
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87 This will install the reference data to ``/data/alphafold_databases``.
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88 To check this has worked, ensure the final folder structure is as
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89 follows:
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90
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91 ::
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92
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93 data/alphafold_databases
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94 ├── bfd
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95 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
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96 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex
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97 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
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98 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex
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99 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
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100 │   └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
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101 ├── mgnify
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102 │   └── mgy_clusters_2018_12.fa
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103 ├── params
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104 │   ├── LICENSE
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105 │   ├── params_model_1.npz
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106 │   ├── params_model_1_ptm.npz
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107 │   ├── params_model_2.npz
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108 │   ├── params_model_2_ptm.npz
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109 │   ├── params_model_3.npz
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110 │   ├── params_model_3_ptm.npz
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111 │   ├── params_model_4.npz
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112 │   ├── params_model_4_ptm.npz
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113 │   ├── params_model_5.npz
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114 │   └── params_model_5_ptm.npz
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115 ├── pdb70
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116 │   ├── md5sum
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117 │   ├── pdb70_a3m.ffdata
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118 │   ├── pdb70_a3m.ffindex
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119 │   ├── pdb70_clu.tsv
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120 │   ├── pdb70_cs219.ffdata
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121 │   ├── pdb70_cs219.ffindex
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122 │   ├── pdb70_hhm.ffdata
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123 │   ├── pdb70_hhm.ffindex
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124 │   └── pdb_filter.dat
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125 ├── pdb_mmcif
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126 │   ├── mmcif_files
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127 │   └── obsolete.dat
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128 ├── uniclust30
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129 │   └── uniclust30_2018_08
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130 └── uniref90
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131 └── uniref90.fasta
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132
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133 JOB DESTINATION
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134 ~~~~~~~~~~~~~~~
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135
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136 Alphafold needs a custom singularity job destination to run. The
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137 destination needs to be configured for singularity, and some extra
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138 singularity params need to be set as seen below.
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139
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140 Specify the job runner. For example, a local runner
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141
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142 ::
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143
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144 <plugin id="alphafold_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
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145
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146 Customise the job destination with required singularity settings. The
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147 settings below are mandatory, but you may include other settings as
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148 needed.
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149
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150 ::
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151
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152 <destination id="alphafold" runner="alphafold_runner">
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153 <param id="dependency_resolution">'none'</param>
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154 <param id="singularity_enabled">true</param>
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155 <param id="singularity_run_extra_arguments">--nv</param>
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156 <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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157 </destination>
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158
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159 Closing
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160 ~~~~~~~
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161
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162 If you are experiencing technical issues, feel free to write to
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163 help@genome.edu.au. We may be able to provide advice on setting up
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164 Alphafold on your compute environment.