simorgh

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy Australia
• Galaxy Main
• Galaxy France
• Galaxy Canada
• Import to another server (≥23.0+ only!)

flowchart TD
  0["Compose text parameter value"];
  1["Compose text parameter value"];
  2["Compose text parameter value"];
  3["Compose text parameter value"];
  4["Compose text parameter value"];
  5["Get PDB file"];
  6["Get PDB file"];
  7["ℹ️ Input Parameter\nI certify that I am NOT using this tool for commercial purposes."];
  style 7 fill:#ded,stroke:#393,stroke-width:4px;
  8["Create text file"];
  0 -->|out1| 8;
  1 -->|out1| 8;
  2 -->|out1| 8;
  3 -->|out1| 8;
  4 -->|out1| 8;
  9["PDBFixer"];
  5 -->|output| 9;
  10["PDBFixer"];
  6 -->|output| 10;
  11["Replace Text"];
  8 -->|outfile| 11;
  12["Text reformatting"];
  9 -->|output| 12;
  13["Text reformatting"];
  10 -->|output| 13;
  14["Colabfold MSA"];
  11 -->|outfile| 14;
  15["SIMORGH"];
  12 -->|outfile| 15;
  7 -->|output| 15;
  98192b3a-6b1a-41fe-896c-545f481e7236["Output\nviz_out_apo"];
  15 --> 98192b3a-6b1a-41fe-896c-545f481e7236;
  style 98192b3a-6b1a-41fe-896c-545f481e7236 stroke:#2c3143,stroke-width:4px;
  d64fa573-c930-42f8-acf8-6a395e56e8f4["Output\npdb_out_apo_multi"];
  15 --> d64fa573-c930-42f8-acf8-6a395e56e8f4;
  style d64fa573-c930-42f8-acf8-6a395e56e8f4 stroke:#2c3143,stroke-width:4px;
  16["SIMORGH"];
  12 -->|outfile| 16;
  7 -->|output| 16;
  a2180ecf-683a-4d9b-9ff4-2350ea0e1769["Output\npdb_out_apo_single"];
  16 --> a2180ecf-683a-4d9b-9ff4-2350ea0e1769;
  style a2180ecf-683a-4d9b-9ff4-2350ea0e1769 stroke:#2c3143,stroke-width:4px;
  0b0dff93-bb3c-4279-a648-5f905f8f705e["Output\nviz_out_apo_single"];
  16 --> 0b0dff93-bb3c-4279-a648-5f905f8f705e;
  style 0b0dff93-bb3c-4279-a648-5f905f8f705e stroke:#2c3143,stroke-width:4px;
  17["SIMORGH"];
  13 -->|outfile| 17;
  7 -->|output| 17;
  66dfb77e-d280-4830-84a6-43ffa177c39f["Output\npdb_out_holo_multi"];
  17 --> 66dfb77e-d280-4830-84a6-43ffa177c39f;
  style 66dfb77e-d280-4830-84a6-43ffa177c39f stroke:#2c3143,stroke-width:4px;
  094ae5d1-7c52-4fe2-a8e3-9fcbd4bb4402["Output\nviz_out_holo"];
  17 --> 094ae5d1-7c52-4fe2-a8e3-9fcbd4bb4402;
  style 094ae5d1-7c52-4fe2-a8e3-9fcbd4bb4402 stroke:#2c3143,stroke-width:4px;
  18["SIMORGH"];
  13 -->|outfile| 18;
  7 -->|output| 18;
  8c8aa601-6ccf-474e-8949-94c2a9a4f05f["Output\npdb_out_holo_single"];
  18 --> 8c8aa601-6ccf-474e-8949-94c2a9a4f05f;
  style 8c8aa601-6ccf-474e-8949-94c2a9a4f05f stroke:#2c3143,stroke-width:4px;
  cb3aaa62-d5a9-428b-ae69-b2db76e4056c["Output\nviz_out_holo_single"];
  18 --> cb3aaa62-d5a9-428b-ae69-b2db76e4056c;
  style cb3aaa62-d5a9-428b-ae69-b2db76e4056c stroke:#2c3143,stroke-width:4px;
  19["Colabfold Alphafold"];
  14 -->|output| 19;
  20["Extract dataset"];
  19 -->|pdb| 20;
  21["SIMORGH"];
  20 -->|output| 21;
  7 -->|output| 21;
  2e4f02ce-e6f2-4e35-aedb-eeb4c95197bc["Output\npdb_out_colabfold_multi"];
  21 --> 2e4f02ce-e6f2-4e35-aedb-eeb4c95197bc;
  style 2e4f02ce-e6f2-4e35-aedb-eeb4c95197bc stroke:#2c3143,stroke-width:4px;
  03e6b954-dddc-4fec-b739-7d76f3553b86["Output\nviz_out_colab"];
  21 --> 03e6b954-dddc-4fec-b739-7d76f3553b86;
  style 03e6b954-dddc-4fec-b739-7d76f3553b86 stroke:#2c3143,stroke-width:4px;
  22["SIMORGH"];
  20 -->|output| 22;
  7 -->|output| 22;
  2d59231a-ff61-4a63-9277-215064291bbc["Output\npdb_out_colabfold_single"];
  22 --> 2d59231a-ff61-4a63-9277-215064291bbc;
  style 2d59231a-ff61-4a63-9277-215064291bbc stroke:#2c3143,stroke-width:4px;
  37c50dfb-faa0-46f7-91da-faff9e12165d["Output\nviz_out_colabfold_single"];
  22 --> 37c50dfb-faa0-46f7-91da-faff9e12165d;
  style 37c50dfb-faa0-46f7-91da-faff9e12165d stroke:#2c3143,stroke-width:4px;

Inputs

Outputs

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

Hands On: Importing a workflow

1. Click on galaxy-workflows-activity Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
2. Click on galaxy-upload Import at the top-right of the screen
3. 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”
4. Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure:

Version History

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/statistics/tutorials/simorgh/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