comparison README.rst @ 16:f9eb041c518c draft

planemo upload for repository https://github.com/usegalaxy-au/tools-au commit ee77734f1800350fa2a6ef28b2b8eade304a456f-dirty

15:a58f7eb0df2c

REFERENCE DATA
~~~~~~~~~~~~~~

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.

To download the AlphaFold reference DBs:

::

   # Set your AlphaFold DB path
   ALPHAFOLD_DB=/data/alphafold_databases

   # Set your target AlphaFold version
   ALPHAFOLD_VERSION=  # e.g. 2.1.2

   # Download repo
   wget https://github.com/deepmind/alphafold/releases/tag/v${ALPHAFOLD_VERSION}.tar.gz
   tar xzf v${ALPHAFOLD_VERSION}.tar.gz

::

   # NOTE: this structure will change between minor AlphaFold versions
   # The tree shown below was updated for v2.3.1

   data/alphafold_databases
   ├── 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
   │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
   │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex

The ``$ALPHAFOLD_DB_ROOT`` directory should now contain this additional file:

::

   data/alphafold_databases
   ├── small_bfd
   │   └── bfd-first_non_consensus_sequences.fasta


**Upgrading database versions**

components that have changed.

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>`_).

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
database is the only component that is persistent, but they are by far the
largest on disk.

16:f9eb041c518c

REFERENCE DATA
~~~~~~~~~~~~~~

Alphafold needs reference data to run. The wrapper expects this data to
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/2.3.1

   # Set your target AlphaFold version
   ALPHAFOLD_VERSION=2.3.1

   # Download repo
   wget https://github.com/deepmind/alphafold/releases/tag/v${ALPHAFOLD_VERSION}.tar.gz
   tar xzf v${ALPHAFOLD_VERSION}.tar.gz

::

   # NOTE: this structure will change between minor AlphaFold versions
   # The tree shown below was updated for v2.3.1

   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
   │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffdata
   │   ├── bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt_cs219.ffindex

The ``$ALPHAFOLD_DB_ROOT`` directory should now contain this additional file:

::

   data/alphafold_databases/2.3.1/
   ├── small_bfd
   │   └── bfd-first_non_consensus_sequences.fasta


**Upgrading database versions**

components that have changed.

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>`_).

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
database is the only component that is persistent, but they are by far the
largest on disk.