Mercurial > repos > galaxy-australia > alphafold2
changeset 4:bc99b0a951ec draft
"planemo upload for repository https://github.com/usegalaxy-au/galaxy-local-tools commit 2d7c3d151feaafc3be33ebb0081ec640680fbb4d-dirty"
| author | galaxy-australia |
|---|---|
| date | Thu, 10 Mar 2022 00:26:56 +0000 |
| parents | 58854e2e6654 |
| children | 138feebde7d3 |
| files | alphafold.xml |
| diffstat | 1 files changed, 9 insertions(+), 3 deletions(-) [+] |
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--- a/alphafold.xml Thu Mar 03 03:29:24 2022 +0000 +++ b/alphafold.xml Thu Mar 10 00:26:56 2022 +0000 @@ -2,7 +2,7 @@ <description>Alphafold v2.0: AI-guided 3D structure prediction of proteins</description> <macros> <token name="@TOOL_VERSION@">2.0.0</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> </macros> <edam_topics> <edam_topic>topic_0082</edam_topic> @@ -49,10 +49,11 @@ --max_template_date=\$DATE --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08 +## use_gpu_relax introduced in AlphaFold v2.1.2 --use_gpu_relax=True && -## Uncomment for "dummy run" - skip alphafold run and read output from test-data +## Uncomment for "dummy" output - read output from test-data ## cp -r '$__tool_directory__/output' . && ## Generate additional outputs ------------ @@ -61,7 +62,12 @@ ## HTML output mkdir -p '${ html.files_path }' && cp '$__tool_directory__/alphafold.html' '${html}' && -cp output/alphafold/ranked_*.pdb '${html.files_path}' +cp output/alphafold/ranked_*.pdb '${html.files_path}' && + +## This is a (hacky) fix for a bug that has appeared in multiple Pulsar servers. +## The working directory ends up two levels deep and the visualization html page +## fails to load the PDB files as static assets. +[ -d working ] && cp -r working/* . ]]></command> <inputs>