Mercurial > repos > galaxy-australia > alphafold2

diff 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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--- a/README.rst	Mon Apr 04 01:46:22 2022 +0000
+++ b/README.rst	Tue Apr 19 00:39:29 2022 +0000
@@ -157,6 +157,18 @@
        <param id="singularity_volumes">"$job_directory:ro,$tool_directory:ro,$job_directory/outputs:rw,$working_directory:rw,/data/alphafold_databases:/data:ro"</param>
    </destination>
 
+CUSTOM PARAMETERS
+~~~~~~~~~~~~~~~~~
+
+A few parameters can be customized with the use of environment variables set in the job destination:
+
+- ``ALPHAFOLD_DB``: path to the reference database root (default ``/data``)
+- ``ALPHAFOLD_AA_LENGTH_MIN``: minimum accepted sequence length (default ``30``)
+- ``ALPHAFOLD_AA_LENGTH_MAX``: maximum accepted sequence length (default ``2000``)
+
+For the last two, these could be set to ``0`` and ``50000`` respectively to remove the valiation entirely.
+
+
 Closing
 ~~~~~~~