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comparison README.rst @ 7:eb085b3dbaf8 draft

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"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 8d9f0ae6af9e8d9313c6cdcc551b24c6c44ae341"
author galaxy-australia
date Tue, 19 Apr 2022 00:39:29 +0000
parents abba603c6ef3
children ca90d17ff51b
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6:04e95886cf24 7:eb085b3dbaf8
155 <param id="singularity_enabled">true</param> 155 <param id="singularity_enabled">true</param>
156 <param id="singularity_run_extra_arguments">--nv</param> 156 <param id="singularity_run_extra_arguments">--nv</param>
157 <param id="singularity_volumes">"$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/alphafold_databases:/data:ro"</param> 157 <param id="singularity_volumes">"$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/alphafold_databases:/data:ro"</param>
158 </destination> 158 </destination>
159 159
160 CUSTOM PARAMETERS
161 ~~~~~~~~~~~~~~~~~
162
163 A few parameters can be customized with the use of environment variables set in the job destination:
164
165 - ``ALPHAFOLD_DB``: path to the reference database root (default ``/data``)
166 - ``ALPHAFOLD_AA_LENGTH_MIN``: minimum accepted sequence length (default ``30``)
167 - ``ALPHAFOLD_AA_LENGTH_MAX``: maximum accepted sequence length (default ``2000``)
168
169 For the last two, these could be set to ``0`` and ``50000`` respectively to remove the valiation entirely.
170
171
160 Closing 172 Closing
161 ~~~~~~~ 173 ~~~~~~~
162 174
163 If you are experiencing technical issues, feel free to write to 175 If you are experiencing technical issues, feel free to write to
164 help@genome.edu.au. We may be able to provide advice on setting up 176 help@genome.edu.au. We may be able to provide advice on setting up