Launch in Tutorial Mode
question
Run Workflow in Galaxy
galaxy-download
Download
flowchart TD
0["ℹ️ Input Dataset\nSILVA Reference"];
style 0 stroke:#2c3143,stroke-width:4px;
1["ℹ️ Input Dataset\nAnguil Soil Sample"];
style 1 stroke:#2c3143,stroke-width:4px;
2["ℹ️ Input Dataset\nPampa Soil Sample"];
style 2 stroke:#2c3143,stroke-width:4px;
3["ℹ️ Input Dataset\nTrainset PDS alignment"];
style 3 stroke:#2c3143,stroke-width:4px;
4["ℹ️ Input Dataset\nTrainset PDS taxonomy"];
style 4 stroke:#2c3143,stroke-width:4px;
5["Merge.files"];
2 -->|output| 5;
1 -->|output| 5;
6["Make.group"];
1 -->|output| 6;
2 -->|output| 6;
7["Unique.seqs"];
5 -->|output| 7;
8["Count.seqs"];
6 -->|output| 8;
7 -->|out_names| 8;
9["Summary.seqs"];
8 -->|seq_count| 9;
7 -->|out_fasta| 9;
10["Screen.seqs"];
7 -->|out_fasta| 10;
8 -->|seq_count| 10;
11["Align.seqs"];
0 -->|output| 11;
10 -->|fasta_out| 11;
12["Summary.seqs"];
10 -->|count_out| 12;
11 -->|out_file| 12;
13["Screen.seqs"];
11 -->|out_file| 13;
10 -->|count_out| 13;
14["Filter.seqs"];
13 -->|fasta_out| 14;
15["Pre.cluster"];
14 -->|filteredfasta| 15;
13 -->|count_out| 15;
16["Classify.seqs"];
15 -->|count_out| 16;
3 -->|output| 16;
15 -->|fasta_out| 16;
4 -->|output| 16;
17["Cluster.split"];
16 -->|taxonomy_out| 17;
15 -->|fasta_out| 17;
15 -->|count_out| 17;
18["Make.shared"];
15 -->|count_out| 18;
17 -->|otulist| 18;
240e2dbf-2dee-455c-9296-795df8c2495d["Output\nmothur_make_shared_shared"];
18 --> 240e2dbf-2dee-455c-9296-795df8c2495d;
style 240e2dbf-2dee-455c-9296-795df8c2495d stroke:#2c3143,stroke-width:4px;
19["Classify.otu"];
15 -->|count_out| 19;
16 -->|taxonomy_out| 19;
17 -->|otulist| 19;
20["Make.biom"];
18 -->|shared| 20;
19 -->|taxonomies| 20;
21["Visualize with Krona"];
19 -->|taxonomies| 21;
Inputs
Input
Label
Input dataset
SILVA Reference
Input dataset
Anguil Soil Sample
Input dataset
Pampa Soil Sample
Input dataset
Trainset PDS alignment
Input dataset
Trainset PDS taxonomy
Outputs
From
Output
Label
toolshed.g2.bx.psu.edu/repos/iuc/mothur_make_shared/mothur_make_shared/1.36.1.0
Make.shared
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
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 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:
Video : Importing a workflow from URL
Version History
Version
Commit
Time
Comments
1
0e0a2f2cc
2024-01-10 15:47:09
Rename metagenomics topic to microbiome
For Admins
Installing the workflow tools
wget https://training.galaxyproject.org/training-material/topics/microbiome/tutorials/general-tutorial/workflows/amplicon.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