Mercurial > repos > galaxy-australia > alphafold2
changeset 11:81d1ef460bb3 draft
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
| author | galaxy-australia |
|---|---|
| date | Fri, 16 Sep 2022 05:13:45 +0000 |
| parents | 072c324f20fc |
| children | 7fbec959cf2b |
| files | README.rst |
| diffstat | 1 files changed, 21 insertions(+), 3 deletions(-) [+] |
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--- a/README.rst Fri Sep 16 02:19:37 2022 +0000 +++ b/README.rst Fri Sep 16 05:13:45 2022 +0000 @@ -75,17 +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 +be present at ``/data/alphafold_databases``. A custom DB root can be read from the ALPHAFOLD_DB environment variable, if set. To download the AlphaFold, reference data, run the following shell script command in the tool directory. :: + # Set databases root + ALPHAFOLD_DB_ROOT=/data/alphafold_databases + # make folders if needed - mkdir /data /data/alphafold_databases + mkdir -p $ALPHAFOLD_DB_ROOT # download ref data - bash scripts/download_all_data.sh /data/alphafold_databases + bash scripts/download_all_data.sh $ALPHAFOLD_DB_ROOT This will install the reference data to ``/data/alphafold_databases``. To check this has worked, ensure the final folder structure is as @@ -133,6 +136,21 @@ └── uniref90 └── uniref90.fasta +In more recent releases of the AlphaFold tool, you will need to download an +additional file to allow the ``reduced_dbs`` option: + +: + bash scripts/download_small_bfd.sh $ALPHAFOLD_DB_ROOT + +The ``$ALPHAFOLD_DB_ROOT`` directory should now contain this additional file: + +: + data/alphafold_databases + ├── small_bfd + │ └── bfd-first_non_consensus_sequences.fasta + + + JOB DESTINATION ~~~~~~~~~~~~~~~