Proteogenomics 2: Database Search

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nUniprot_cRAP_SAV_indel_translatedbed.FASTA"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Collection\nMGF Collection"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nReference Protein Accessions"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["Identification Parameters"];
  4["Search GUI"];
  0 -->|output| 4;
  3 -->|Identification_Parameters_File| 4;
  1 -->|output| 4;
  1e6409c7-5606-4399-9e7c-7d314f62faa7["Output\nSearch GUI on input dataset(s)"];
  4 --> 1e6409c7-5606-4399-9e7c-7d314f62faa7;
  style 1e6409c7-5606-4399-9e7c-7d314f62faa7 stroke:#2c3143,stroke-width:4px;
  5["Peptide Shaker"];
  4 -->|searchgui_results| 5;
  a9c129c1-29e4-44dc-92ba-46dcbf621a69["Output\noutput_certificate"];
  5 --> a9c129c1-29e4-44dc-92ba-46dcbf621a69;
  style a9c129c1-29e4-44dc-92ba-46dcbf621a69 stroke:#2c3143,stroke-width:4px;
  6ed85517-2c68-4c99-8b91-545d210ff76d["Output\nmzidentML"];
  5 --> 6ed85517-2c68-4c99-8b91-545d210ff76d;
  style 6ed85517-2c68-4c99-8b91-545d210ff76d stroke:#2c3143,stroke-width:4px;
  31acbe56-7d85-4979-936a-737987acead7["Output\noutput_psm"];
  5 --> 31acbe56-7d85-4979-936a-737987acead7;
  style 31acbe56-7d85-4979-936a-737987acead7 stroke:#2c3143,stroke-width:4px;
  6["mz to sqlite"];
  5 -->|mzidentML| 6;
  c4df335c-977b-4c07-92f5-5edb42ddeee9["Output\nMz to sqlite"];
  6 --> c4df335c-977b-4c07-92f5-5edb42ddeee9;
  style c4df335c-977b-4c07-92f5-5edb42ddeee9 stroke:#2c3143,stroke-width:4px;
  7["Removing reference proteins"];
  5 -->|output_psm| 7;
  5 -->|output_psm| 7;
  2 -->|output| 7;
  6ab25e80-3805-42c3-8895-550e278b2a3a["Output\nRemoving reference proteins"];
  7 --> 6ab25e80-3805-42c3-8895-550e278b2a3a;
  style 6ab25e80-3805-42c3-8895-550e278b2a3a stroke:#2c3143,stroke-width:4px;
  8["Selecting sequence with length >6 and <30"];
  7 -->|output| 8;
  babe6986-f3d0-4687-93a1-d28fbaea1efa["Output\nSelecting sequence with length >6 and <30"];
  8 --> babe6986-f3d0-4687-93a1-d28fbaea1efa;
  style babe6986-f3d0-4687-93a1-d28fbaea1efa stroke:#2c3143,stroke-width:4px;
  9["Peptides_for_BlastP_analysis"];
  8 -->|output| 9;
  d01167ef-d3f1-4dfd-89df-29a9c1e9acb8["Output\nPeptides_for_BlastP_analysis"];
  9 --> d01167ef-d3f1-4dfd-89df-29a9c1e9acb8;
  style d01167ef-d3f1-4dfd-89df-29a9c1e9acb8 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/proteomics/tutorials/proteogenomics-dbsearch/workflows/galaxy-workflow-mouse_rnaseq_dbsearch.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