Mercurial > repos > galaxy-australia > alphafold2
comparison README.rst @ 11:81d1ef460bb3 draft
planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 01b5c58f98b79c9b11757013dc6e69ea06dbd709
author | galaxy-australia |
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date | Fri, 16 Sep 2022 05:13:45 +0000 |
parents | ca90d17ff51b |
children | 7fbec959cf2b |
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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 |