MakeAFakeInput

contributing-create-new-tutorial/galaxy-workflow-makeafakeinput

Author(s)

Version
4
Last updated
Jan 23, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
contributing

Features
Tutorial
Creating a new tutorial
Other workflows associated with this material
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00040
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  0["ℹ️ Input Dataset\nSRR891268_R1_20M.fastq.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nSRR891268_R2_20M.fastq.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  10["Unique"];
  9 -->|out_file1| 10;
  11["Text transformation"];
  10 -->|outfile| 11;
  12["Concatenate datasets"];
  6 -->|out_file1| 12;
  11 -->|output| 12;
  13["Unique"];
  12 -->|out_file1| 13;
  14["seqtk_subseq"];
  0 -->|output| 14;
  13 -->|outfile| 14;
  15["Text transformation"];
  13 -->|outfile| 15;
  16["seqtk_subseq"];
  1 -->|output| 16;
  15 -->|output| 16;
  2["FASTQ to Tabular"];
  0 -->|output| 2;
  3["Cutadapt"];
  0 -->|output| 3;
  1 -->|output| 3;
  4["Cut"];
  2 -->|output_file| 4;
  5["Bowtie2"];
  3 -->|out1| 5;
  3 -->|out2| 5;
  6["Select random lines"];
  4 -->|output| 6;
  7["BAM-to-SAM"];
  5 -->|output| 7;
  8["Filter"];
  7 -->|output1| 8;
  9["Cut"];
  8 -->|out_file1| 9;

Inputs

Input Label
Input dataset SRR891268_R1_20M.fastq.gz
Input dataset SRR891268_R2_20M.fastq.gz

Outputs

From Output Label

Tools

Tool Links
Cut1
Filter1
random_lines1
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bam_to_sam/bam_to_sam/2.0.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/iuc/seqtk/seqtk_subseq/1.3.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/1.16.5 View in ToolShed

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

Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
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 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:

Video: Importing a workflow from URL

Version History

Version Commit Time Comments
4 667ff3de9 2020-01-22 10:59:29 annotation
3 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
2 faf6d298a 2019-12-12 13:02:33 unflatten workflows
1 2e196e930 2019-08-02 10:41:17 move workflow file to repo and minor tweaks

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/contributing/tutorials/create-new-tutorial/workflows/Galaxy-Workflow-MakeAFakeInput.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