Intro to Genome Assembly

Run Workflow in Galaxy

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

flowchart TD
  0["ℹ️ Input Dataset\nmutant_R1.fastq"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nmutant_R2.fastq"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["ℹ️ Input Dataset\nwildtype.fna"];
  style 2 stroke:#2c3143,stroke-width:4px;
  3["FastQC"];
  0 -->|output| 3;
  22a51e6e-2e5f-4415-a127-e0b1c179a1b1["Output\nfastqc_html"];
  3 --> 22a51e6e-2e5f-4415-a127-e0b1c179a1b1;
  style 22a51e6e-2e5f-4415-a127-e0b1c179a1b1 stroke:#2c3143,stroke-width:4px;
  51ec8c05-eb47-4359-9120-0eca1a6d5c2f["Output\nfastqc_txt"];
  3 --> 51ec8c05-eb47-4359-9120-0eca1a6d5c2f;
  style 51ec8c05-eb47-4359-9120-0eca1a6d5c2f stroke:#2c3143,stroke-width:4px;
  4["FastQC"];
  1 -->|output| 4;
  5["FASTQ interlacer"];
  0 -->|output| 5;
  1 -->|output| 5;
  225edf5f-3b90-4f84-a38a-5c786000a3fc["Output\noutput_pairs"];
  5 --> 225edf5f-3b90-4f84-a38a-5c786000a3fc;
  style 225edf5f-3b90-4f84-a38a-5c786000a3fc stroke:#2c3143,stroke-width:4px;
  dae90093-ae96-4bb2-824d-c92b61585096["Output\noutput_singles"];
  5 --> dae90093-ae96-4bb2-824d-c92b61585096;
  style dae90093-ae96-4bb2-824d-c92b61585096 stroke:#2c3143,stroke-width:4px;
  6["MultiQC"];
  3 -->|text_file| 6;
  4 -->|text_file| 6;
  85e3704a-859d-4657-b3d7-9b67e4981d21["Output\nmultiqc_stats"];
  6 --> 85e3704a-859d-4657-b3d7-9b67e4981d21;
  style 85e3704a-859d-4657-b3d7-9b67e4981d21 stroke:#2c3143,stroke-width:4px;
  fab7e06a-604e-4432-b0ed-b63157a8643b["Output\nmultiqc_report"];
  6 --> fab7e06a-604e-4432-b0ed-b63157a8643b;
  style fab7e06a-604e-4432-b0ed-b63157a8643b stroke:#2c3143,stroke-width:4px;
  7["velveth"];
  5 -->|outfile_pairs| 7;
  607a214d-9137-4e73-9b73-954c79678937["Output\nvelveth_out"];
  7 --> 607a214d-9137-4e73-9b73-954c79678937;
  style 607a214d-9137-4e73-9b73-954c79678937 stroke:#2c3143,stroke-width:4px;
  8["velvetg"];
  7 -->|out_file1| 8;
  b0cf3779-6199-42c9-963f-a733559f90bb["Output\nvelvet_contigs"];
  8 --> b0cf3779-6199-42c9-963f-a733559f90bb;
  style b0cf3779-6199-42c9-963f-a733559f90bb stroke:#2c3143,stroke-width:4px;
  54926701-ccae-4143-b649-b7e08e1c6a8e["Output\nvelvet_stats"];
  8 --> 54926701-ccae-4143-b649-b7e08e1c6a8e;
  style 54926701-ccae-4143-b649-b7e08e1c6a8e stroke:#2c3143,stroke-width:4px;
  9["Quast"];
  2 -->|output| 9;
  8 -->|contigs| 9;
  0babe959-4d63-4838-9e18-4526b3dd0db5["Output\nquast_report_html"];
  9 --> 0babe959-4d63-4838-9e18-4526b3dd0db5;
  style 0babe959-4d63-4838-9e18-4526b3dd0db5 stroke:#2c3143,stroke-width:4px;
  f41c43c4-763c-42bc-b36e-9ea76e7752c2["Output\nquast_report_pdf"];
  9 --> f41c43c4-763c-42bc-b36e-9ea76e7752c2;
  style f41c43c4-763c-42bc-b36e-9ea76e7752c2 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/assembly/tutorials/general-introduction/workflows/assembly-general-introduction.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