Mercurial > repos > galaxy-australia > alphafold2
diff README.rst @ 16:f9eb041c518c draft
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty
| author | galaxy-australia |
|---|---|
| date | Mon, 03 Apr 2023 01:00:42 +0000 |
| parents | d00e15139065 |
| children |
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--- a/README.rst Fri Mar 10 02:48:07 2023 +0000 +++ b/README.rst Mon Apr 03 01:00:42 2023 +0000 @@ -75,18 +75,20 @@ ~~~~~~~~~~~~~~ Alphafold needs reference data to run. The wrapper expects this data to -be present at ``/data/alphafold_databases``. A custom path will be read from -the ``ALPHAFOLD_DB`` environment variable, if set. +be present at ``/$ALPHAFOLD_DB/TOOL_MINOR_VERSION``. +Where ``ALPHAFOLD_DB`` is a custom path that will be read from +the ``ALPHAFOLD_DB`` environment variable (defaulting to ``/data``). +And TOOL_MINOR_VERSION is the alphafold version, e.g. ``2.3.1``. To download the AlphaFold reference DBs: :: # Set your AlphaFold DB path - ALPHAFOLD_DB=/data/alphafold_databases + ALPHAFOLD_DB=/data/alphafold_databases/2.3.1 # Set your target AlphaFold version - ALPHAFOLD_VERSION= # e.g. 2.1.2 + ALPHAFOLD_VERSION=2.3.1 # Download repo wget https://github.com/deepmind/alphafold/releases/tag/v${ALPHAFOLD_VERSION}.tar.gz @@ -110,7 +112,7 @@ # NOTE: this structure will change between minor AlphaFold versions # The tree shown below was updated for v2.3.1 - data/alphafold_databases + data/alphafold_databases/2.3.1/ ├── bfd │ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffdata │ ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_a3m.ffindex @@ -176,7 +178,7 @@ :: - data/alphafold_databases + data/alphafold_databases/2.3.1/ ├── small_bfd │ └── bfd-first_non_consensus_sequences.fasta @@ -193,7 +195,7 @@ If you wish to continue hosting prior versions of the tool, you must maintain the reference DBs for each version. The ``ALPHAFOLD_DB`` environment variable must then be set respectively for each tool version in your job conf (on Galaxy -AU this is currently `configured with TPV<https://github.com/usegalaxy-au/infrastructure/blob/master/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml#L1515-L1554>`_). +AU this is currently `configured with TPV <https://github.com/usegalaxy-au/infrastructure/blob/master/files/galaxy/dynamic_job_rules/production/total_perspective_vortex/tools.yml#L1515-L1554>`_). To minimize redundancy between DB version, we have symlinked the database components that are unchanging between versions. In ``v2.1.2 -> v2.3.1`` the BFD