biopipelines
A modular and user-friendly Python framework for protein and ligand engineering workflows on SLURM clusters
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- CODEOWNERS
- pull_request_template.md
- __init__.py
- _layout.py
- _TEMPLATE.py
- _TEMPLATE_CHECKLIST.md
- _weights_cache.py
- admet_ai.py
- af2bind.py
- aggrescan3d.py
- aizynthfinder.py
- alphafold.py
- angle.py
- apbs.py
- base_config.py
- bayesian_adjuster.py
- bioemu.py
- biopipelines_io.py
- boltz2.py
- boltzgen.py
- cabsflex.py
- cli.py
- combinatorics.py
- compound_datasets.py
- compound_library.py
- config_editor.py
- config_manager.py
- conformational_change.py
- consensus.py
- contacts.py
- converters.py
- datastream.py
- datastream_resolver.py
- diffdock.py
- distance.py
- distance_selector.py
- dna_encoder.py
- dssp.py
- dynamicbind.py
- ensemble_analysis.py
- entities.py
- esmfold.py
- esmfold2.py
- extract_metrics.py
- file_paths.py
- folders.py
- fpocket.py
- frame2seq.py
- fuse.py
- gems.py
- gnina.py
- guiding_potentials.py
- hbdesigner.py
- id_map_utils.py
- id_patterns.py
- input_standardization.py
- lasermpnn.py
- ligand.py
- ligand_mpnn.py
- ligand_utils.py
- load.py
- mmseqs2.py
- mock.py
- msa.py
- mutagenesis.py
- mutation_composer.py
- mutation_profiler.py
- neuralplexer.py
- openbabel.py
- openmm.py
- p2rank.py
- panda.py
- pdb.py
- pdb_parser.py
- pipeline.py
- placer.py
- plip.py
- plm_sol.py
- plot.py
- pocketgen.py
- pool.py
- pose_change.py
- posebusters.py
- prodigy.py
- prolif.py
- protein_mpnn.py
- pymol.py
- rbs_designer.py
- rcsb.py
- rdkit_descriptors.py
- reduce.py
- remap.py
- rfdiffusion.py
- rfdiffusion2.py
- rfdiffusion3.py
- rfdiffusion_allatom.py
- rtmscore.py
- sasa.py
- schedulers.py
- scripting.py
- scripting_api.py
- sele_utils.py
- selection.py
- sequence.py
- sequence_metric_correlation.py
- stitch_sequences.py
- stream_slicers.py
- table.py
- table_utils.py
- thermompnn.py
- uniprot.py
- vespag.py
- warm.py
- xtb.py
- figure1_ubiquitin_pipeline.png
- figure3_boltz2_compound_screening.png
- analysis.md
- cheminformatics.md
- data_management.md
- inputs_io.md
- msas.md
- sequence_design.md
- statistics.md
- structure_generation.md
- structure_prediction.md
- developer_manual.md
- index.md
- tool_index.md
- tool_reference.md
- user_manual.md
- build_image.sh
- Containerfile
- share_image.sh
- _containers.yaml
- admet_ai.pip.daint.txt
- admet_ai.pip.txt
- admet_ai.yaml
- af2bind.yaml
- Aggrescan3D.colab.yaml
- Aggrescan3D.yaml
- aizynthfinder.pip.txt
- aizynthfinder.yaml
- alphafold.pip.daint.txt
- apbs.colab.yaml
- apbs.yaml
- bioemu.pip.daint.txt
- bioemu.yaml
- biopipelines.daint.yaml
- biopipelines.pip.daint.txt
- biopipelines.yaml
- Boltz2Env.pip.txt
- Boltz2Env.yaml
- boltzgen.pip.txt
- boltzgen.yaml
- CABSflex.colab.yaml
- CABSflex.yaml
- diffdock.colab.yaml
- diffdock.pip.colab.txt
- diffdock.pip.txt
- diffdock.yaml
- dssp.colab.yaml
- dssp.yaml
- dynamicbind.colab.yaml
- dynamicbind.pip.1.txt
- dynamicbind.pip.2.txt
- dynamicbind.pip.colab.1.txt
- dynamicbind.pip.colab.2.txt
- dynamicbind.yaml
- dynamicbind_relax.colab.yaml
- dynamicbind_relax.yaml
- esmfold.cluster.yaml
- esmfold.colab.yaml
- esmfold.pip.colab.1.txt
- esmfold.pip.colab.2.txt
- esmfold2.pip.txt
- esmfold2.yaml
- foundry.pip.txt
- foundry.yaml
- fpocket.colab.yaml
- fpocket.yaml
- frame2seq.colab.yaml
- frame2seq.pip.colab.txt
- frame2seq.pip.txt
- frame2seq.yaml
- gems.colab.yaml
- gems.yaml
- gnina.yaml
- hbdesigner.cpu.pip.txt
- hbdesigner.cpu.yaml
- hbdesigner.gpu.pip.txt
- hbdesigner.gpu.yaml
- lasermpnn.colab.pip.txt
- lasermpnn.colab.yaml
- lasermpnn.cpu.pip.txt
- lasermpnn.cpu.yaml
- lasermpnn.gpu.pip.txt
- lasermpnn.gpu.yaml
- ligandmpnn_env.pip.cluster.txt
- ligandmpnn_env.pip.colab.txt
- ligandmpnn_env.pip.daint.txt
- ligandmpnn_env.yaml
- MutationEnv.yaml
- neuralplexer.colab.yaml
- neuralplexer.pip.1.txt
- neuralplexer.pip.2.txt
- neuralplexer.pip.3.txt
- neuralplexer.pip.colab.1.txt
- neuralplexer.pip.colab.2.txt
- neuralplexer.pip.colab.3.txt
- neuralplexer.yaml
- openmm.colab.yaml
- openmm.yaml
- p2rank.colab.yaml
- p2rank.yaml
- placer.yaml
- plip.colab.yaml
- plip.pip.1.txt
- plip.pip.colab.1.txt
- plip.yaml
- plm_sol.pip.txt
- plm_sol.yaml
- pocketgen.colab.yaml
- pocketgen.pip.1.txt
- pocketgen.pip.2.txt
- pocketgen.pip.colab.1.txt
- pocketgen.pip.colab.2.txt
- pocketgen.yaml
- posebusters.pip.txt
- posebusters.yaml
- prodigy.colab.yaml
- prodigy.yaml
- prolif.colab.yaml
- prolif.yaml
- ProteinEnv.cluster.yaml
- ProteinEnv.colab.yaml
- rbs_designer.cluster.yaml
- rbs_designer.colab.yaml
- reduce.colab.yaml
- reduce.yaml
- rfdiffusion_allatom.pip.txt
- rtmscore.colab.yaml
- rtmscore.yaml
- SE3nv.cluster.yaml
- SE3nv.colab.yaml
- SE3nv.daint.yaml
- SE3nv.pip.cluster.txt
- SE3nv.pip.colab.txt
- SE3nv.pip.daint.txt
- thermompnn.colab.yaml
- thermompnn.pip.colab.txt
- thermompnn.yaml
- vespag.colab.yaml
- vespag.pip.colab.txt
- vespag.pip.txt
- vespag.yaml
- xtb.yaml
- bayesian_directed_evolution.ipynb
- bayesian_directed_evolution_results.ipynb
- compound_admet_triage.ipynb
- compound_admet_triage_results.ipynb
- compound_screening.ipynb
- compound_screening_results.ipynb
- conformational_flexibility.ipynb
- conformational_flexibility_results.ipynb
- FRET.ipynb
- FRET_results.ipynb
- interaction_profiling.ipynb
- interaction_profiling_results.ipynb
- iterative_binding_optimization.ipynb
- iterative_binding_optimization_results.ipynb
- kinase_LID_redesign.ipynb
- kinase_LID_redesign_results.ipynb
- msa_free_folding.ipynb
- msa_free_folding_results.ipynb
- pocket_validation.ipynb
- pocket_validation_results.ipynb
- ppi_interface_energetics.ipynb
- ppi_interface_energetics_results.ipynb
- ubiquitin.ipynb
- ubiquitin_results.ipynb
- urolithin_target_search.ipynb
- urolithin_target_search_results.ipynb
- alphafold_params.py
- boltz2_params.py
- boltzgen_params.py
- cabsflex_params.py
- chain_native_inputs.py
- dna_encoder_params.py
- gnina_params.py
- ligand_mpnn_params.py
- mmseqs2_params.py
- posebusters_params.py
- protein_mpnn_params.py
- pymol_params.py
- rbs_designer_params.py
- rfdiffusion3_params.py
- rfdiffusion_allatom_params.py
- rfdiffusion_params.py
- _mmseqs2_cpu_server.py
- _mmseqs2_verify.py
- _reinstall_rtmscore.py
- boltz2.py
- boltzgen_refold.py
- CABSflex.py
- compound_library_TrpR.cdxml
- compound_screening.py
- daint_packed_design.py
- denovo_dopamine_boltzgen.py
- FRET.py
- FRET_angle.py
- FRET_mutagenesis.py
- gnina_docking.py
- install_daint.py
- install_mmseqs2_databases.py
- install_tools.py
- iterative_binding_optimization.py
- iterative_binding_optimization_deduplication.py
- iterative_binding_optimization_gnina.py
- iterative_binding_optimization_posebusters.py
- kinase_LID_redesign.py
- kinase_LID_redesign_parallel.py
- mmseqs_boltz2.py
- multiple_submission.py
- parallel_pool.py
- rfd3_pmpnn_ligandmpnn_boltz2.py
- rfd_pmpnn_af2_one_line.py
- saturation_mutagenesis.py
- ubiquitin.py
- README.md
- .gitignore
- cluster.md
- colab.md
- daint.md
- development.md
- log.sh
- pipelines.md
- README.md
- resources.md.template
- README.md
- template.ipynb
- template.py
- count_atoms.py
- filter_structures.py
- README.md
- README.md
- README.md
- _pipe_template.py
- colabfold_setup_databases.sh
- materialize_filtered_map_table.py
- mmseqs2_client.sh
- mmseqs2_server_cpu.sh
- mmseqs2_server_gpu.sh
- pipe_admet_ai.py
- pipe_af2bind.py
- pipe_aggrescan3d.py
- pipe_aizynthfinder.py
- pipe_alphafold_confidence.py
- pipe_alphafold_msas.py
- pipe_alphafold_queries.py
- pipe_angle.py
- pipe_apbs.py
- pipe_bayesian_adjuster.py
- pipe_bioemu.py
- pipe_boltz_compounds.py
- pipe_boltz_config_unified.py
- pipe_boltz_direct_sequence_config.py
- pipe_boltz_msa_copy.py
- pipe_boltz_postprocessing.py
- pipe_boltz_results.py
- pipe_boltzgen.py
- pipe_boltzgen_config.py
- pipe_boltzgen_import.py
- pipe_boltzgen_merge.py
- pipe_cabsflex.py
- pipe_check_completion.py
- pipe_compound_images.py
- pipe_compound_library.py
- pipe_conformational_change.py
- pipe_consensus.py
- pipe_contacts.py
- pipe_csv_to_fasta.py
- pipe_diffdock_build_csv.py
- pipe_diffdock_postprocess.py
- pipe_distance.py
- pipe_distance_selector.py
- pipe_dna_encoder.py
- pipe_dssp.py
- pipe_dynamicbind_build_csv.py
- pipe_dynamicbind_movie.py
- pipe_dynamicbind_postprocess.py
- pipe_ensemble_analysis.py
- pipe_esmfold2_inference.py
- pipe_esmfold2_postprocessing.py
- pipe_esmfold_inference.py
- pipe_esmfold_postprocessing.py
- pipe_extract_metrics.py
- pipe_fa_to_csv_fasta.py
- pipe_filter_execution.py
- pipe_fpocket.py
- pipe_frame2seq.py
- pipe_fuse_queries.py
- pipe_gems.py
- pipe_gnina.py
- pipe_hbdesigner.py
- pipe_hbdesigner_constraints.py
- pipe_lasermpnn.py
- pipe_lasermpnn_bfactor.py
- pipe_ligand.py
- pipe_lmpnn_runtime_positions.py
- pipe_load_output_filter.py
- pipe_mmseqs2_sequences.py
- pipe_mock.py
- pipe_msa.py
- pipe_mutagenesis.py
- pipe_mutagenesis_msa.py
- pipe_mutation_composer.py
- pipe_mutation_profiler.py
- pipe_neuralplexer_postprocess.py
- pipe_neuralplexer_stage.py
- pipe_openbabel.py
- pipe_openmm.py
- pipe_p2rank.py
- pipe_panda.py
- pipe_pdb.py
- pipe_placer_driver.py
- pipe_placer_postprocess.py
- pipe_plip.py
- pipe_plm_sol.py
- pipe_plot.py
- pipe_pmpnn_fixed_positions.py
- pipe_pmpnn_table.py
- pipe_pocketgen_driver.py
- pipe_pocketgen_postprocess.py
- pipe_pocketgen_stage.py
- pipe_pool.py
- pipe_pose_change.py
- pipe_posebusters.py
- pipe_prodigy.py
- pipe_prolif.py
- pipe_propagate_missing.py
- pipe_pymol.py
- pipe_rbs_designer.py
- pipe_rcsb_search.py
- pipe_rdkit_descriptors.py
- pipe_reduce.py
- pipe_remap.py
- pipe_rfdaa_prepare_ligand.py
- pipe_rfdiffusion3_build_inputs.py
- pipe_rfdiffusion3_postprocess.py
- pipe_rfdiffusion3_table.py
- pipe_rfdiffusion_contigs.py
- pipe_rfdiffusion_table.py
- pipe_rtmscore.py
- pipe_sasa.py
- pipe_scripting.py
- pipe_selection.py
- pipe_sequence.py
- pipe_sequence_metric_correlation.py
- pipe_smiles_library.py
- pipe_smiles_properties.py
- pipe_stitch_sequences.py
- pipe_thermompnn.py
- pipe_uniprot.py
- pipe_unsanitize_ids.py
- pipe_update_structures_map.py
- pipe_vespag.py
- pipe_xtb.py
- resolve_hbdesigner_constraints.py
- resolve_lmpnn_positions.py
- resolve_rfdiffusion_contigs.py
- resolve_stream_ids.py
- resolve_stream_item.sh
- resolve_table_column.py
- fasta.py
- grids.py
- images.py
- plots.py
- streams.py
- structures.py
- tables.py
- README.md
- container_backend.md
- daint_backend.md
- SKILL.md
- README.md
- config.local.yaml
- config.lsf_local.yaml
- config.pbs_local.yaml
- config.slurm_local.yaml
- config.slurm_packed.yaml
- __init__.py
- _helpers.py
- test_alphafold_params.py
- test_boltz2_params.py
- test_boltzgen_params.py
- test_cabsflex_params.py
- test_dna_encoder_params.py
- test_gnina_params.py
- test_ligand_mpnn_params.py
- test_mmseqs2_params.py
- test_new_wrappers_params.py
- test_pool_params.py
- test_posebusters_params.py
- test_protein_mpnn_params.py
- test_pymol_params.py
- test_rbs_designer_params.py
- test_rfdiffusion3_params.py
- test_rfdiffusion_allatom_params.py
- test_rfdiffusion_params.py
- __init__.py
- conftest.py
- test_aizynthfinder_params.py
- test_bayesian_adjuster.py
- test_cabsflex_colab.py
- test_combinatorics.py
- test_config_overlay.py
- test_consensus.py
- test_datastream.py
- test_datastream_chunks.py
- test_folders.py
- test_id_filter_audit.py
- test_id_map_utils.py
- test_id_patterns.py
- test_internal_and_folder.py
- test_ligand.py
- test_ligand_vendor.py
- test_load_multiple_folder.py
- test_missing_propagation.py
- test_mmseqs2_http_aliases.py
- test_mock.py
- test_mpnn_upstream_missing.py
- test_openbabel.py
- test_panda.py
- test_parallel.py
- test_parallel_pack.py
- test_pdb.py
- test_pdb_parser_cif.py
- test_pipeline_generation.py
- test_plane_side_selection.py
- test_pmpnn_chain_positions.py
- test_pocket_validation_wiring.py
- test_pool.py
- test_provenance.py
- test_range_pattern_runtime_ids.py
- test_rcsb_stream_search.py
- test_rdkit_strain.py
- test_remap.py
- test_resolve_selection_in_sequence.py
- test_resolve_selection_union.py
- test_resolve_stream_ids_valid_set.py
- test_schedulers.py
- test_scripting_runtime.py
- test_scripting_scripts_folder.py
- test_sequence.py
- test_service.py
- test_shell_safety.py
- test_stitch_sequences.py
- test_stream_slicers.py
- test_table.py
- test_table_reference_provenance.py
- CHANGELOG.md
- check_tool_edits.py
- tool_changelog.yaml
- .gitattributes
- .gitignore
- .gitlab-ci.yml
- .pre-commit-config.yaml
- .readthedocs.yaml
- check-updates
- config.cluster.yaml
- config.colab.yaml
- config.container.yaml
- config.daint.yaml
- config.local.yaml
- CONTRIBUTING.md
- Dockerfile.container
- LICENSE
- mkdocs.yml
- pyproject.toml
- README.md
- requirements-docs.txt
- resubmit
- run
- submit
# Installation Guide
1. Get the code
git clone https://github.com/locbp-uzh/biopipelines
Downloads the entire project code from GitHub to your computer.
cd biopipelines
Moves into the project folder you just downloaded.
2. Docker
Easy RecommendedPrerequisites
- Git Needed to download the project code from GitHub.
- Docker Desktop Needed to build and run containers. Install it and keep it running in the background.
docker build -f Dockerfile.container -t biopipelines .
Builds a runnable image based on the Dockerfile.
docker run -p 8080:80 biopipelines
Runs the built image as an actual container.
Run docker compose ps to check the containers are Up. If the README mentions a port, open http://localhost:PORT in your browser.
3. Python
EasyPrerequisites
pip install .
Installs the package published on PyPI directly — no need to clone the source.
jupyter notebook
Launches Jupyter in your browser so you can open and run the notebook (.ipynb) files.
If it runs without errors and prints output in the terminal, it worked.
// repository documentation
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