Essential genes detection with Transposon insertion sequencing

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nTnseq-Tutorial-reads.fastqsanger.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\ncondition_barcodes.fasta"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nconstruct_barcodes.fasta"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nstaph_aur.fasta"];
  style 3 stroke:#2c3143,stroke-width:4px;
  4["ℹ️ Input Dataset\nstaph_aur.gff3"];
  style 4 stroke:#2c3143,stroke-width:4px;
  5["Cutadapt"];
  0 -->|output| 5;
  1 -->|output| 5;
  6["Nucleotide subsequence search"];
  3 -->|output| 6;
  7["Convert GFF3"];
  4 -->|output| 7;
  8["Cutadapt"];
  5 -->|split_output| 8;
  9["Cut"];
  6 -->|output| 9;
  10["Cut"];
  6 -->|output| 10;
  11["Cutadapt"];
  8 -->|out1| 11;
  12["Compute"];
  10 -->|out_file1| 12;
  13["Cutadapt"];
  11 -->|out1| 13;
  2 -->|output| 13;
  14["Cut"];
  12 -->|out_file1| 14;
  15["Cutadapt"];
  13 -->|split_output| 15;
  16["Map with Bowtie for Illumina"];
  3 -->|output| 16;
  15 -->|out1| 16;
  17["bamCoverage"];
  16 -->|output| 17;
  18["Join"];
  17 -->|outFileName| 18;
  9 -->|out_file1| 18;
  19["Join"];
  17 -->|outFileName| 19;
  14 -->|out_file1| 19;
  20["Cut"];
  18 -->|output| 20;
  21["Cut"];
  19 -->|output| 21;
  22["Sort"];
  20 -->|out_file1| 22;
  23["Compute"];
  21 -->|out_file1| 23;
  24["Cut"];
  23 -->|out_file1| 24;
  25["Sort"];
  24 -->|out_file1| 25;
  26["Join"];
  22 -->|outfile| 26;
  25 -->|outfile| 26;
  27["Compute"];
  26 -->|output| 27;
  28["Cut"];
  27 -->|out_file1| 28;
  29["Sort"];
  28 -->|out_file1| 29;
  30["Gumbel"];
  7 -->|output| 30;
  29 -->|outfile| 30;
  31["Filter"];
  30 -->|sites| 31;
  32["Extract Dataset"];
  31 -->|out_file1| 32;
  8796f62f-4676-4ad2-b085-7597f894c32c["Output\ncontrol"];
  32 --> 8796f62f-4676-4ad2-b085-7597f894c32c;
  style 8796f62f-4676-4ad2-b085-7597f894c32c stroke:#2c3143,stroke-width:4px;
  33["Extract Dataset"];
  31 -->|out_file1| 33;
  bd014de4-708e-419c-bd1e-8bf350661aad["Output\ncondition"];
  33 --> bd014de4-708e-419c-bd1e-8bf350661aad;
  style bd014de4-708e-419c-bd1e-8bf350661aad stroke:#2c3143,stroke-width:4px;
  34["Join"];
  32 -->|output| 34;
  33 -->|output| 34;
  5cdfb5c9-c677-41dc-a838-c4a61d62f5be["Output\nessential_both"];
  34 --> 5cdfb5c9-c677-41dc-a838-c4a61d62f5be;
  style 5cdfb5c9-c677-41dc-a838-c4a61d62f5be stroke:#2c3143,stroke-width:4px;
  35["Join"];
  32 -->|output| 35;
  33 -->|output| 35;
  8b2b65ea-37c3-43d2-b416-38f8f920fbd9["Output\nessential_control"];
  35 --> 8b2b65ea-37c3-43d2-b416-38f8f920fbd9;
  style 8b2b65ea-37c3-43d2-b416-38f8f920fbd9 stroke:#2c3143,stroke-width:4px;
  36["Join"];
  32 -->|output| 36;
  33 -->|output| 36;
  37639319-b053-4fbc-bf61-fd3e38263502["Output\nessential_condition"];
  36 --> 37639319-b053-4fbc-bf61-fd3e38263502;
  style 37639319-b053-4fbc-bf61-fd3e38263502 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/genome-annotation/tutorials/tnseq/workflows/essential-genes-detection-transposon-insertion-sequencing-workflow.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