GTN Proteogemics3 Novel Peptide Analysis

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\nEdited_Mus_Musculus.GRCm38.86"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\npeptides for blast"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nPSM Report"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nmz_sqlite"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\ngenomic mapping sqlite db"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["NCBI BLAST+ blastp"];
  1 -->|output| 5;
  88461c74-1312-41d5-bd54-e7d7297ccd76["Output\nBLASTP_results"];
  5 --> 88461c74-1312-41d5-bd54-e7d7297ccd76;
  style 88461c74-1312-41d5-bd54-e7d7297ccd76 stroke:#2c3143,stroke-width:4px;
  6["PSM_Novel_Peptides"];
  5 -->|output1| 6;
  2 -->|output| 6;
  29c9a368-a7e6-4e8b-81ca-131f63293093["Output\nPSM_Novel_Peptides"];
  6 --> 29c9a368-a7e6-4e8b-81ca-131f63293093;
  style 29c9a368-a7e6-4e8b-81ca-131f63293093 stroke:#2c3143,stroke-width:4px;
  7["Novel_Peptides"];
  6 -->|output| 7;
  56954668-7aac-423a-89af-aecf2b405b94["Output\nNovel_Peptides"];
  7 --> 56954668-7aac-423a-89af-aecf2b405b94;
  style 56954668-7aac-423a-89af-aecf2b405b94 stroke:#2c3143,stroke-width:4px;
  8["Peptide Genomic Coodinate"];
  4 -->|output| 8;
  3 -->|output| 8;
  7 -->|output| 8;
  60fd3e41-8cb7-4a49-b585-2a43117e9cf8["Output\nPeptide Genomic Coodinate on input dataset(s)"];
  8 --> 60fd3e41-8cb7-4a49-b585-2a43117e9cf8;
  style 60fd3e41-8cb7-4a49-b585-2a43117e9cf8 stroke:#2c3143,stroke-width:4px;
  9["PepPointer"];
  8 -->|peptide_bed| 9;
  0 -->|output| 9;
  3c410bed-ff79-4774-b75c-48659d291160["Output\nPepPointer on input dataset(s)"];
  9 --> 3c410bed-ff79-4774-b75c-48659d291160;
  style 3c410bed-ff79-4774-b75c-48659d291160 stroke:#2c3143,stroke-width:4px;
  10["Final_Summary_Novel_Peptides"];
  9 -->|classified| 10;
  6 -->|output| 10;
  50e64c95-cd68-47cb-9e0c-b3714b2f2431["Output\nFinal_Summary_Novel_Peptides"];
  10 --> 50e64c95-cd68-47cb-9e0c-b3714b2f2431;
  style 50e64c95-cd68-47cb-9e0c-b3714b2f2431 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-novel-peptide-analysis/workflows/galaxy-workflow-mouse_novel_peptide_analysis.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