Mercurial > repos > galaxy-australia > alphafold2

comparison README.rst @ 11:81d1ef460bb3 draft

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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 ca90d17ff51b
children 7fbec959cf2b
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10:072c324f20fc 11:81d1ef460bb3
73 73
74 REFERENCE DATA 74 REFERENCE DATA
75 ~~~~~~~~~~~~~~ 75 ~~~~~~~~~~~~~~
76 76
77 Alphafold needs reference data to run. The wrapper expects this data to 77 Alphafold needs reference data to run. The wrapper expects this data to
78 be present at ``/data/alphafold_databases``. A custom path will be read from 78 be present at ``/data/alphafold_databases``. A custom DB root can be read from
79 the ALPHAFOLD_DB environment variable, if set. To download the AlphaFold, 79 the ALPHAFOLD_DB environment variable, if set. To download the AlphaFold,
80 reference data, run the following shell script command in the tool directory. 80 reference data, run the following shell script command in the tool directory.
81 81
82 :: 82 ::
83 83
84 # Set databases root
85 ALPHAFOLD_DB_ROOT=/data/alphafold_databases
86
84 # make folders if needed 87 # make folders if needed
85 mkdir /data /data/alphafold_databases 88 mkdir -p $ALPHAFOLD_DB_ROOT
86 89
87 # download ref data 90 # download ref data
88 bash scripts/download_all_data.sh /data/alphafold_databases 91 bash scripts/download_all_data.sh $ALPHAFOLD_DB_ROOT
89 92
90 This will install the reference data to ``/data/alphafold_databases``. 93 This will install the reference data to ``/data/alphafold_databases``.
91 To check this has worked, ensure the final folder structure is as 94 To check this has worked, ensure the final folder structure is as
92 follows: 95 follows:
93 96
131 ├── uniclust30 134 ├── uniclust30
132 │   └── uniclust30_2018_08 135 │   └── uniclust30_2018_08
133 └── uniref90 136 └── uniref90
134 └── uniref90.fasta 137 └── uniref90.fasta
135 138
139 In more recent releases of the AlphaFold tool, you will need to download an
140 additional file to allow the ``reduced_dbs`` option:
141
142 :
143 bash scripts/download_small_bfd.sh $ALPHAFOLD_DB_ROOT
144
145 The ``$ALPHAFOLD_DB_ROOT`` directory should now contain this additional file:
146
147 :
148 data/alphafold_databases
149 ├── small_bfd
150 │   └── bfd-first_non_consensus_sequences.fasta
151
152
153
136 JOB DESTINATION 154 JOB DESTINATION
137 ~~~~~~~~~~~~~~~ 155 ~~~~~~~~~~~~~~~
138 156
139 Alphafold needs a custom singularity job destination to run. The 157 Alphafold needs a custom singularity job destination to run. The
140 destination needs to be configured for singularity, and some extra 158 destination needs to be configured for singularity, and some extra