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comparison README.rst @ 8:ca90d17ff51b draft

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
author galaxy-australia
date Fri, 19 Aug 2022 00:29:16 +0000
parents eb085b3dbaf8
children 81d1ef460bb3
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7:eb085b3dbaf8 8:ca90d17ff51b
7 Alphafold requires a customised compute environment to run. The machine 7 Alphafold requires a customised compute environment to run. The machine
8 needs a GPU, and access to a 2.2 Tb reference data store. 8 needs a GPU, and access to a 2.2 Tb reference data store.
9 9
10 This document is designed to provide details on the compute environment 10 This document is designed to provide details on the compute environment
11 required for Alphafold operation, and the Galaxy job destination 11 required for Alphafold operation, and the Galaxy job destination
12 settings to run the wrapper. 12 settings to run the wrapper. We strongly suggest reading this entire document
13 to ensure that your setup is compatible with the hardware that you are
14 deploying to.
13 15
14 For full details on Alphafold requirements, see 16 For full details on Alphafold requirements, see
15 https://github.com/deepmind/alphafold. 17 https://github.com/deepmind/alphafold.
16 18
17 HARDWARE 19 HARDWARE
161 ~~~~~~~~~~~~~~~~~ 163 ~~~~~~~~~~~~~~~~~
162 164
163 A few parameters can be customized with the use of environment variables set in the job destination: 165 A few parameters can be customized with the use of environment variables set in the job destination:
164 166
165 - ``ALPHAFOLD_DB``: path to the reference database root (default ``/data``) 167 - ``ALPHAFOLD_DB``: path to the reference database root (default ``/data``)
166 - ``ALPHAFOLD_AA_LENGTH_MIN``: minimum accepted sequence length (default ``30``) 168 - ``ALPHAFOLD_USE_GPU [True/False]``: set to ``False`` to disable GPU dependency (defaults to ``True``)
167 - ``ALPHAFOLD_AA_LENGTH_MAX``: maximum accepted sequence length (default ``2000``) 169 - ``ALPHAFOLD_AA_LENGTH_MIN``: minimum accepted sequence length (default ``0``)
168 170 - ``ALPHAFOLD_AA_LENGTH_MAX``: maximum accepted sequence length (default ``0`` - no validation)
169 For the last two, these could be set to ``0`` and ``50000`` respectively to remove the valiation entirely.
170
171 171
172 Closing 172 Closing
173 ~~~~~~~ 173 ~~~~~~~
174 174
175 If you are experiencing technical issues, feel free to write to 175 If you are experiencing technical issues, feel free to write to