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comparison alphafold.xml @ 6:04e95886cf24 draft

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"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
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' . &&