Proteomics: database handling including mycoplasma

Run Workflow in Galaxy

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

flowchart TD
  0["Protein Database Downloader"];
  1["Protein Database Downloader"];
  2["Protein Database Downloader"];
  3["Protein Database Downloader"];
  4["Protein Database Downloader"];
  5["Protein Database Downloader"];
  6["Protein Database Downloader"];
  7["Protein Database Downloader"];
  8["FASTA-to-Tabular"];
  2 -->|output_database| 8;
  9["FASTA Merge Files and Filter Unique Sequences"];
  5 -->|output_database| 9;
  4 -->|output_database| 9;
  3 -->|output_database| 9;
  1 -->|output_database| 9;
  0 -->|output_database| 9;
  6 -->|output_database| 9;
  10["Add column"];
  8 -->|output| 10;
  11["FASTA-to-Tabular"];
  9 -->|output| 11;
  12["Tabular-to-FASTA"];
  10 -->|out_file1| 12;
  13["Add column"];
  11 -->|output| 13;
  14["Tabular-to-FASTA"];
  13 -->|out_file1| 14;
  15["FASTA Merge Files and Filter Unique Sequences"];
  12 -->|output| 15;
  7 -->|output_database| 15;
  14 -->|output| 15;
  16["DecoyDatabase"];
  15 -->|output| 16;

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

• 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/database-handling/workflows/wf_database-handling_mycoplasma.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