Mercurial > repos > galaxy-australia > alphafold2
comparison README.rst @ 8:ca90d17ff51b draft
"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 03537aada92b5fff565ff48dd47c81462c5df47e"
author | galaxy-australia |
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date | Fri, 19 Aug 2022 00:29:16 +0000 |
parents | eb085b3dbaf8 |
children | 81d1ef460bb3 |
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7:eb085b3dbaf8 | 8:ca90d17ff51b |
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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 |