Mercurial > repos > galaxy-australia > alphafold2
comparison alphafold.xml @ 6:04e95886cf24 draft
"planemo upload for repository https://github.com/usegalaxy-au/tools-au commit 724a7a389c878dded1c0332f3b6e507e0c4cd52a-dirty"
| author | galaxy-australia |
|---|---|
| date | Mon, 04 Apr 2022 01:46:22 +0000 |
| parents | 138feebde7d3 |
| children | eb085b3dbaf8 |
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| 5:138feebde7d3 | 6:04e95886cf24 |
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| 27 | 27 |
| 28 #elif $fasta_or_text.input_mode == 'textbox': | 28 #elif $fasta_or_text.input_mode == 'textbox': |
| 29 echo '$fasta_or_text.fasta_text' > input.fasta && | 29 echo '$fasta_or_text.fasta_text' > input.fasta && |
| 30 #end if | 30 #end if |
| 31 | 31 |
| 32 python3 '$__tool_directory__/validate_fasta.py' input.fasta && | 32 python3 '$__tool_directory__/validate_fasta.py' input.fasta |
| 33 --min_length \${ALPHAFOLD_AA_LENGTH_MIN:-30} | |
| 34 --max_length \${ALPHAFOLD_AA_LENGTH_MAX:-2000} | |
| 35 > alphafold.fasta && | |
| 33 | 36 |
| 34 ## env vars ------------------------------- | 37 ## env vars ------------------------------- |
| 35 export TF_FORCE_UNIFIED_MEMORY=1 && | 38 export TF_FORCE_UNIFIED_MEMORY=1 && |
| 36 export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 && | 39 export XLA_PYTHON_CLIENT_MEM_FRACTION=4.0 && |
| 37 export DATE=`date +"%Y-%m-%d"` && | 40 export DATE=`date +"%Y-%m-%d"` && |
| 47 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files | 50 --template_mmcif_dir \${ALPHAFOLD_DB:-/data}/pdb_mmcif/mmcif_files |
| 48 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat | 51 --obsolete_pdbs_path \${ALPHAFOLD_DB:-/data}/pdb_mmcif/obsolete.dat |
| 49 --max_template_date=\$DATE | 52 --max_template_date=\$DATE |
| 50 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt | 53 --bfd_database_path \${ALPHAFOLD_DB:-/data}/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt |
| 51 --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08 | 54 --uniclust30_database_path \${ALPHAFOLD_DB:-/data}/uniclust30/uniclust30_2018_08/uniclust30_2018_08 |
| 52 ## use_gpu_relax introduced in AlphaFold v2.1.2 | 55 ## Param introduced in AlphaFold v2.1.2: |
| 53 --use_gpu_relax=True | 56 --use_gpu_relax=True |
| 54 && | 57 && |
| 55 | 58 |
| 56 ## Uncomment for "dummy" output - read output from test-data | 59 ## Uncomment for "dummy" output - read output from test-data |
| 57 ## cp -r '$__tool_directory__/output' . && | 60 ## cp -r '$__tool_directory__/output' . && |