Zauberkugel
computational-chemistry-zauberkugel/main-workflow
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flowchart TD 0["ℹ️ Input Dataset\nQuery ligand"]; style 0 stroke:#2c3143,stroke-width:4px; 1["ℹ️ Input Dataset\nPharmacophore library"]; style 1 stroke:#2c3143,stroke-width:4px; 2["Ligand ionization state generation"]; 0 -->|output| 2; 3["Splitting ePharmaLib into individual pharmacophores"]; 1 -->|output| 3; 4[" Low-energy ligand conformer search"]; 2 -->|outfile| 4; 5["Pharmacophore alignment"]; 4 -->|outfile| 5; 3 -->|list_output_generic| 5; 6["Concatenating the pharmacophore alignment scores"]; 5 -->|score_result_file| 6; 7["Ranking the predicted protein targets according to the Tversky index 10th column"]; 6 -->|out_file1| 7;
Inputs
Input | Label |
---|---|
Input dataset | Query ligand |
Input dataset | Pharmacophore library |
Outputs
From | Output | Label |
---|---|---|
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh/3.1.1+galaxy1 | Add hydrogen atoms | Ligand ionization state generation |
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 | Split file | Splitting ePharmaLib into individual pharmacophores |
toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf/2020.03.4+galaxy0 | RDConf: Low-energy ligand conformer search | Low-energy ligand conformer search |
toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit/1.0.4+galaxy0 | Pharmacophore alignment | |
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1 | Concatenate datasets | Concatenating the pharmacophore alignment scores |
sort1 | Sort | Ranking the predicted protein targets according to the Tversky index (10th column) |
Tools
To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.
Importing into Galaxy
Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!Hands-on: Importing a workflow
- Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
- Click on galaxy-upload Import at the top-right of the screen
- Provide your workflow
- Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
- Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
- Click the Import workflow button
Below is a short video demonstrating how to import a workflow from GitHub using this procedure:
Video: Importing a workflow from URL
Version History
Version | Commit | Time | Comments |
---|---|---|---|
3 | b70afe303 | 2022-02-15 13:25:54 | annotate workflow for gtn linting |
2 | 506069da4 | 2022-02-11 12:36:16 | pretty print pharmacophore workflow |
1 | fdd280bcf | 2022-02-08 20:03:56 | Add files via upload |
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/zauberkugel/workflows/main_workflow.ga -O workflow.ga workflow-to-tools -w workflow.ga -o tools.yaml shed-tools install -g GALAXY -a API_KEY -t tools.yaml workflow-install -g GALAXY -a API_KEY -w workflow.ga --publish-workflows