Blockclust 1.1.0 Clustering

transcriptomics-small_ncrna_clustering/blockclust-clustering

Author(s)

Version
4
Last updated
Oct 8, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
transcriptomics

Features
Tutorial
Small Non-coding RNA Clustering using BlockClust
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00254
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\nblockclust_input"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["Samtools sort"];
  0 -->|output| 1;
  2["BlockClust"];
  1 -->|output1| 2;
  39f8722a-8444-42f8-8104-f81201804c9c["Output\ntags_bed"];
  2 --> 39f8722a-8444-42f8-8104-f81201804c9c;
  style 39f8722a-8444-42f8-8104-f81201804c9c stroke:#2c3143,stroke-width:4px;
  3["Sort"];
  2 -->|tags_bed| 3;
  4["blockbuster"];
  3 -->|outfile| 4;
  95c21ce9-e988-44b9-978e-10a27b74d18e["Output\nblockbuster_out"];
  4 --> 95c21ce9-e988-44b9-978e-10a27b74d18e;
  style 95c21ce9-e988-44b9-978e-10a27b74d18e stroke:#2c3143,stroke-width:4px;
  5["BlockClust"];
  4 -->|output| 5;
  241feec1-9ffd-4d28-9b65-e58850198c6d["Output\nmodel_based_pred_bed"];
  5 --> 241feec1-9ffd-4d28-9b65-e58850198c6d;
  style 241feec1-9ffd-4d28-9b65-e58850198c6d stroke:#2c3143,stroke-width:4px;
  287b4bae-55a1-4f38-b1c3-62ae60b4d950["Output\nclusters_bed"];
  5 --> 287b4bae-55a1-4f38-b1c3-62ae60b4d950;
  style 287b4bae-55a1-4f38-b1c3-62ae60b4d950 stroke:#2c3143,stroke-width:4px;

Inputs

Input Label
Input dataset blockclust_input

Outputs

From Output Label
Input dataset blockclust_input
toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0 BlockClust
toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2 blockbuster
toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0 BlockClust

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 View in ToolShed
toolshed.g2.bx.psu.edu/repos/devteam/samtools_sort/samtools_sort/2.0.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/blockbuster/blockbuster/0.1.2 View in ToolShed
toolshed.g2.bx.psu.edu/repos/rnateam/blockclust/blockclust/1.1.0 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 2e2cb42d8 2020-10-04 11:59:11 add tests from workflow-testing for blockclust and rna-seq-viz-with-volcano-plot, edit workflows
3 667ff3de9 2020-01-22 10:59:29 annotation
2 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
1 0afe265cf 2018-12-12 08:44:45 initial version of training material for small ncRNA clustering using blockclust

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/small_ncrna_clustering/workflows/blockclust_clustering.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