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annotate README.md @ 0:7ae9d78b06f5 draft

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"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 7b79778448363aa8c9b14604337e81009e461bd2-dirty"
author galaxy-australia
date Fri, 28 Jan 2022 04:56:29 +0000
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2 # Alphafold compute setup
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4 ## Overview
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6 Alphafold requires a customised compute environment to run. The machine needs a GPU, and access to a 2.2 Tb reference data store.
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8 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.
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10 For full details on Alphafold requirements, see https://github.com/deepmind/alphafold.
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12 <br>
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14 ### HARDWARE
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16 The machine is recommended to have the following specs:
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17 - 12 cores
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18 - 80 Gb RAM
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19 - 2.5 Tb storage
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20 - A fast Nvidia GPU.
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22 As a minimum, the Nvidia GPU must have 8Gb RAM. It also requires ***unified memory*** to be switched on. <br>
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23 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.
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25 <br>
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27 ### ENVIRONMENT
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29 This wrapper runs Alphafold as a singularity container. The following software are needed:
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31 - [Singularity](https://sylabs.io/guides/3.0/user-guide/installation.html)
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32 - [NVIDIA Container Toolkit](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/install-guide.html)
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34 As Alphafold uses an Nvidia GPU, the NVIDIA Container Toolkit is needed. This makes the GPU available inside the running singularity container.
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36 To check that everything has been set up correctly, run the following
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38 ```
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39 singularity run --nv docker://nvidia/cuda:11.0-base nvidia-smi
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40 ```
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42 If you can see something similar to this output (details depend on your GPU), it has been set up correctly.
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44 ```
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45 +-----------------------------------------------------------------------------+
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46 | NVIDIA-SMI 470.57.02 Driver Version: 470.57.02 CUDA Version: 11.4 |
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47 |-------------------------------+----------------------+----------------------+
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48 | GPU Name Persistence-M| Bus-Id Disp.A | Volatile Uncorr. ECC |
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49 | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
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50 | | | MIG M. |
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51 |===============================+======================+======================|
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52 | 0 Tesla T4 Off | 00000000:00:05.0 Off | 0 |
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53 | N/A 49C P0 28W / 70W | 0MiB / 15109MiB | 0% Default |
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54 | | | N/A |
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55 +-------------------------------+----------------------+----------------------+
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57 +-----------------------------------------------------------------------------+
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58 | Processes: |
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59 | GPU GI CI PID Type Process name GPU Memory |
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60 | ID ID Usage |
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61 |=============================================================================|
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62 | No running processes found |
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63 +-----------------------------------------------------------------------------+
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64 ```
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67 <br>
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69 ### REFERENCE DATA
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71 Alphafold needs reference data to run. The wrapper expects this data to be present at `/data/alphafold_databases`. <br>
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72 To download, run the following shell script command in the tool directory.
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74 ```
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75 # make folders if needed
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76 mkdir /data /data/alphafold_databases
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78 # download ref data
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79 bash scripts/download_all_data.sh /data/alphafold_databases
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80 ```
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82 This will install the reference data to `/data/alphafold_databases`. To check this has worked, ensure the final folder structure is as follows:
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84 ```
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85 data/alphafold_databases
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86 ├── bfd
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87 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata
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88 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex
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89 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
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90 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex
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91 │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffdata
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92 │   └── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_hhm.ffindex
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93 ├── mgnify
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94 │   └── mgy_clusters_2018_12.fa
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95 ├── params
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96 │   ├── LICENSE
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97 │   ├── params_model_1.npz
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98 │   ├── params_model_1_ptm.npz
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99 │   ├── params_model_2.npz
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100 │   ├── params_model_2_ptm.npz
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101 │   ├── params_model_3.npz
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102 │   ├── params_model_3_ptm.npz
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103 │   ├── params_model_4.npz
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104 │   ├── params_model_4_ptm.npz
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105 │   ├── params_model_5.npz
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106 │   └── params_model_5_ptm.npz
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107 ├── pdb70
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108 │   ├── md5sum
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109 │   ├── pdb70_a3m.ffdata
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110 │   ├── pdb70_a3m.ffindex
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111 │   ├── pdb70_clu.tsv
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112 │   ├── pdb70_cs219.ffdata
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113 │   ├── pdb70_cs219.ffindex
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114 │   ├── pdb70_hhm.ffdata
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115 │   ├── pdb70_hhm.ffindex
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116 │   └── pdb_filter.dat
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117 ├── pdb_mmcif
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118 │   ├── mmcif_files
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119 │   └── obsolete.dat
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120 ├── uniclust30
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121 │   └── uniclust30_2018_08
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122 └── uniref90
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123 └── uniref90.fasta
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124 ```
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125
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126
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127 <br>
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128
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129 ### JOB DESTINATION
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130
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131 Alphafold needs a custom singularity job destination to run.
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132 The destination needs to be configured for singularity, and some
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133 extra singularity params need to be set as seen below.
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134
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135 Specify the job runner. For example, a local runner
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136
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137 ```
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138 <plugin id="alphafold_runner" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
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139 ```
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140
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141 Customise the job destination with required singularity settings. <br>
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142 The settings below are mandatory, but you may include other settings as needed.
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143
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144 ```
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145 <destination id="alphafold" runner="alphafold_runner">
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146 <param id="dependency_resolution">'none'</param>
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147 <param id="singularity_enabled">true</param>
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148 <param id="singularity_run_extra_arguments">--nv</param>
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149 <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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150 </destination>
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151 ```
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152
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153 <br>
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154
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155 ### Closing
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156
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157 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.