Workflow constructed from history 'Computer assignment RNA seq analysis and visualisation -BMW2 - attempt 3'

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\np53_mock_1.csv"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\np53_mock_2.csv"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\np53_mock_3.csv"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\np53_mock_4.csv"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\np53_IR_1.csv"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["ℹ️ Input Dataset\np53_IR_2.csv"];
  style 5 stroke:#2c3143,stroke-width:4px;
  6["ℹ️ Input Dataset\np53_IR_3.csv"];
  style 6 stroke:#2c3143,stroke-width:4px;
  7["ℹ️ Input Dataset\np53_IR_4.csv"];
  style 7 stroke:#2c3143,stroke-width:4px;
  8["ℹ️ Input Dataset\nnull_mock_1.csv"];
  style 8 stroke:#2c3143,stroke-width:4px;
  9["ℹ️ Input Dataset\nnull_mock_2.csv"];
  style 9 stroke:#2c3143,stroke-width:4px;
  10["ℹ️ Input Dataset\nnull_IR_1.csv"];
  style 10 stroke:#2c3143,stroke-width:4px;
  11["ℹ️ Input Dataset\nnull_IR_2.csv"];
  style 11 stroke:#2c3143,stroke-width:4px;
  12["ℹ️ Input Dataset\nInput dataset"];
  style 12 stroke:#2c3143,stroke-width:4px;
  13["ℹ️ Input Dataset\nInput dataset"];
  style 13 stroke:#2c3143,stroke-width:4px;
  14["ℹ️ Input Dataset\nInput dataset"];
  style 14 stroke:#2c3143,stroke-width:4px;
  15["ℹ️ Input Dataset\nInput dataset"];
  style 15 stroke:#2c3143,stroke-width:4px;
  16["ℹ️ Input Dataset\nInput dataset"];
  style 16 stroke:#2c3143,stroke-width:4px;
  17["ℹ️ Input Dataset\nInput dataset"];
  style 17 stroke:#2c3143,stroke-width:4px;
  18["ℹ️ Input Dataset\nInput dataset"];
  style 18 stroke:#2c3143,stroke-width:4px;
  19["ℹ️ Input Dataset\nInput dataset"];
  style 19 stroke:#2c3143,stroke-width:4px;
  20["ℹ️ Input Dataset\nInput dataset"];
  style 20 stroke:#2c3143,stroke-width:4px;
  21["ℹ️ Input Dataset\nInput dataset"];
  style 21 stroke:#2c3143,stroke-width:4px;
  22["ℹ️ Input Dataset\nInput dataset"];
  style 22 stroke:#2c3143,stroke-width:4px;
  23["ℹ️ Input Dataset\nInput dataset"];
  style 23 stroke:#2c3143,stroke-width:4px;
  24["ℹ️ Input Dataset\nInput dataset"];
  style 24 stroke:#2c3143,stroke-width:4px;
  25["ℹ️ Input Dataset\nInput dataset"];
  style 25 stroke:#2c3143,stroke-width:4px;
  26["ℹ️ Input Dataset\nAnnotation file"];
  style 26 stroke:#2c3143,stroke-width:4px;
  27["ℹ️ Input Dataset\nheader"];
  style 27 stroke:#2c3143,stroke-width:4px;
  28["ℹ️ Input Dataset\nGSE71176_sample_metadata.txt"];
  style 28 stroke:#2c3143,stroke-width:4px;
  29["ℹ️ Input Dataset\nGSE71176_variable_metadata.txt"];
  style 29 stroke:#2c3143,stroke-width:4px;
  30["ℹ️ Input Dataset\nInput dataset"];
  style 30 stroke:#2c3143,stroke-width:4px;
  31["ℹ️ Input Dataset\nInput dataset"];
  style 31 stroke:#2c3143,stroke-width:4px;
  32["ℹ️ Input Dataset\nInput dataset"];
  style 32 stroke:#2c3143,stroke-width:4px;
  33["ℹ️ Input Dataset\nInput dataset"];
  style 33 stroke:#2c3143,stroke-width:4px;
  34["ℹ️ Input Dataset\nInput dataset"];
  style 34 stroke:#2c3143,stroke-width:4px;
  35["ℹ️ Input Dataset\nInput dataset"];
  style 35 stroke:#2c3143,stroke-width:4px;
  36["DESeq2"];
  18 -->|output| 36;
  19 -->|output| 36;
  20 -->|output| 36;
  21 -->|output| 36;
  24 -->|output| 36;
  25 -->|output| 36;
  14 -->|output| 36;
  15 -->|output| 36;
  16 -->|output| 36;
  17 -->|output| 36;
  22 -->|output| 36;
  23 -->|output| 36;
  22 -->|output| 36;
  23 -->|output| 36;
  24 -->|output| 36;
  25 -->|output| 36;
  14 -->|output| 36;
  15 -->|output| 36;
  16 -->|output| 36;
  17 -->|output| 36;
  18 -->|output| 36;
  19 -->|output| 36;
  20 -->|output| 36;
  21 -->|output| 36;
  37["DESeq2"];
  22 -->|output| 37;
  23 -->|output| 37;
  24 -->|output| 37;
  25 -->|output| 37;
  14 -->|output| 37;
  15 -->|output| 37;
  16 -->|output| 37;
  17 -->|output| 37;
  18 -->|output| 37;
  19 -->|output| 37;
  20 -->|output| 37;
  21 -->|output| 37;
  18 -->|output| 37;
  19 -->|output| 37;
  20 -->|output| 37;
  21 -->|output| 37;
  24 -->|output| 37;
  25 -->|output| 37;
  14 -->|output| 37;
  15 -->|output| 37;
  16 -->|output| 37;
  17 -->|output| 37;
  22 -->|output| 37;
  23 -->|output| 37;
  38["Gene length and GC content"];
  26 -->|output| 38;
  39["Filter"];
  36 -->|deseq_out| 39;
  40["Table Compute"];
  36 -->|vst_out| 40;
  41["Table Compute"];
  36 -->|vst_out| 41;
  42["Volcano Plot"];
  37 -->|deseq_out| 42;
  43["Join"];
  36 -->|deseq_out| 43;
  38 -->|length| 43;
  44["Sort"];
  39 -->|out_file1| 44;
  45["Join"];
  36 -->|vst_out| 45;
  40 -->|table| 45;
  46["Compute"];
  43 -->|output| 46;
  47["Annotate DESeq2/DEXSeq output tables"];
  26 -->|output| 47;
  44 -->|outfile| 47;
  48["Join"];
  45 -->|output| 48;
  41 -->|table| 48;
  49["Cut"];
  46 -->|out_file1| 49;
  50["Cut"];
  46 -->|out_file1| 50;
  51["Concatenate datasets"];
  27 -->|output| 51;
  47 -->|output| 51;
  52["Compute"];
  48 -->|output| 52;
  53["goseq"];
  49 -->|out_file1| 53;
  50 -->|out_file1| 53;
  54["goseq"];
  49 -->|out_file1| 54;
  50 -->|out_file1| 54;
  55["Volcano Plot"];
  51 -->|out_file1| 55;
  56["Cut"];
  51 -->|out_file1| 56;
  57["Sort"];
  52 -->|out_file1| 57;
  58["Select first"];
  57 -->|outfile| 58;
  59["Cut"];
  58 -->|out_file1| 59;
  60["Cut"];
  59 -->|out_file1| 60;
  61["heatmap2"];
  59 -->|out_file1| 61;
  62["heatmap2"];
  59 -->|out_file1| 62;
  63["heatmap2"];
  59 -->|out_file1| 63;
  64["Multivariate"];
  59 -->|out_file1| 64;
  35 -->|output| 64;
  60 -->|out_file1| 64;
  65["Multivariate"];
  59 -->|out_file1| 65;
  35 -->|output| 65;
  60 -->|out_file1| 65;

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/transcriptomics/tutorials/rna-seq-analysis-clustering-viz/workflows/RNA_seq_analysis_and_visualisation.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