trinity NG

Run Workflow in Galaxy

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

flowchart TD
  20["Trinotate"];
  18 -->|transdecoder_pep| 20;
  21["Differential expression analysis"];
  19 -->|TPM_no_norm_gene| 21;
  3 -->|output| 21;
  22["Extract and cluster differentially expressed transcripts"];
  21 -->|DE_results| 22;
  19 -->|norm_TMM| 22;
  3 -->|output| 22;
  23["Partition genes into expression clusters"];
  22 -->|rdata| 23;
  1["ℹ️ Input Collection\nCollection of R2 reads"];
  style 1 stroke:#2c3143,stroke-width:4px;
  0["ℹ️ Input Collection\nCollection of R1 reads"];
  style 0 stroke:#2c3143,stroke-width:4px;
  3["ℹ️ Input Dataset\nSamples description"];
  style 3 stroke:#2c3143,stroke-width:4px;
  2["Describe samples"];
  5["FastQC"];
  1 -->|output| 5;
  4["FastQC"];
  0 -->|output| 4;
  7["MultiQC"];
  5 -->|text_file| 7;
  4 -->|text_file| 7;
  6["Trimmomatic"];
  0 -->|output| 6;
  1 -->|output| 6;
  9["FastQC"];
  6 -->|fastq_out_r2_paired| 9;
  8["FastQC"];
  6 -->|fastq_out_r1_paired| 8;
  11["MultiQC"];
  9 -->|text_file| 11;
  8 -->|text_file| 11;
  10["Trinity"];
  6 -->|fastq_out_r2_paired| 10;
  6 -->|fastq_out_r1_paired| 10;
  13["Build expression matrix"];
  12 -->|genes_counts_rsem| 13;
  12["Align reads and estimate abundance"];
  10 -->|assembled_transcripts| 12;
  6 -->|fastq_out_r2_paired| 12;
  6 -->|fastq_out_r1_paired| 12;
  15["Filter low expression transcripts"];
  10 -->|assembled_transcripts| 15;
  13 -->|TPM_no_norm_gene| 15;
  14["RNASeq samples quality check"];
  13 -->|trans_counts| 14;
  3 -->|output| 14;
  17["Align reads and estimate abundance"];
  15 -->|filtered| 17;
  6 -->|fastq_out_r1_paired| 17;
  6 -->|fastq_out_r2_paired| 17;
  16["Compute contig Ex90N50 statistic and Ex90 transcript count"];
  10 -->|assembled_transcripts| 16;
  13 -->|trans_counts| 16;
  19["Build expression matrix"];
  17 -->|genes_counts_rsem| 19;
  18["TransDecoder"];
  15 -->|filtered| 18;

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/transcriptomics/tutorials/full-de-novo/workflows/main_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