GTN Proteogemics2 Database Search

Run Workflow in Galaxy

• Galaxy Europe
• Galaxy Main
• Galaxy France
• Galaxy Australia
• 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["Search GUI"];
  0 -->|output| 3;
  1 -->|output| 3;
  d14f9481-80db-4c15-8afc-6fa38ef61deb["Output\nSearch GUI on input dataset(s)"];
  3 --> d14f9481-80db-4c15-8afc-6fa38ef61deb;
  style d14f9481-80db-4c15-8afc-6fa38ef61deb stroke:#2c3143,stroke-width:4px;
  4["Peptide Shaker"];
  3 -->|searchgui_results| 4;
  afe0f1a5-28bb-44bd-b32b-c634aa2154f3["Output\nPeptide Shaker on input dataset(s): mzidentML file"];
  4 --> afe0f1a5-28bb-44bd-b32b-c634aa2154f3;
  style afe0f1a5-28bb-44bd-b32b-c634aa2154f3 stroke:#2c3143,stroke-width:4px;
  5["mz to sqlite"];
  4 -->|mzidentML| 5;
  1 -->|output| 5;
  0 -->|output| 5;
  b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9["Output\nmz to sqlite on input dataset(s)"];
  5 --> b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9;
  style b43a2136-cf59-4fb0-bb2b-0d5b446c8ba9 stroke:#2c3143,stroke-width:4px;
  6["Removing reference proteins"];
  4 -->|output_psm| 6;
  4 -->|output_psm| 6;
  2 -->|output| 6;
  a06ad5fa-9a00-4867-b976-3745c5e59c80["Output\nRemoving reference proteins"];
  6 --> a06ad5fa-9a00-4867-b976-3745c5e59c80;
  style a06ad5fa-9a00-4867-b976-3745c5e59c80 stroke:#2c3143,stroke-width:4px;
  7["Selecting sequence with length >6 and <30"];
  6 -->|output| 7;
  b71e5417-2864-4712-b5c1-c90725976baf["Output\nSelecting sequence with length >6 and <30"];
  7 --> b71e5417-2864-4712-b5c1-c90725976baf;
  style b71e5417-2864-4712-b5c1-c90725976baf stroke:#2c3143,stroke-width:4px;
  8["Peptides for BlastP analysis"];
  7 -->|output| 8;
  1ac3c776-8095-4db1-8518-3643dc081006["Output\nPeptides_for_BlastP_analysis"];
  8 --> 1ac3c776-8095-4db1-8518-3643dc081006;
  style 1ac3c776-8095-4db1-8518-3643dc081006 stroke:#2c3143,stroke-width:4px;

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

• 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:

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