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galaxyproject / usegalaxy-tools

usegalaxy.* common tools
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alphafold2: either repair index or deprecate the tool #531

Open jennaj opened 2 years ago

jennaj commented 2 years ago

toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold/2.1.2+galaxy0

Most current version installed at UseGalaxy.org and UseGalaxy.eu. No version is installed at UseGalaxy.org.au (?).

Toolshed was last updated in April to this same version: https://toolshed.g2.bx.psu.edu/view/galaxy-australia/alphafold2/eb085b3dbaf8

Errors like this:

E0712 09:45:17.378200 47656303294336 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70 Traceback (most recent call last): File "/app/alphafold/run_alphafold.py", line 445, in app.run(main) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/opt/conda/lib/python3.7/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/app/alphafold/run_alphafold.py", line 353, in main databases=[FLAGS.pdb70_database_path]) File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 57, in init raise ValueError(f'Could not find HHsearch database {database_path}') ValueError: Could not find HHsearch database /data/pdb70/pdb70

jennaj commented 1 year ago

Update: works at usegalaxy.org.au only for now

Updated version available https://toolshed.g2.bx.psu.edu/view/galaxy-australia/alphafold2/7fbec959cf2b