CTB Workflow

computational-chemistry-cheminformatics/main-workflow

Author(s)

Version
6
Last updated
Feb 19, 2020
License
None Specified, defaults to CC-BY-4.0
Tags
computational-chemistry

Features
Tutorial
Protein-ligand docking
Workflow Testing
Tests: ❌
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00031
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on WorkflowHub
Launch in Tutorial Mode
Download 
flowchart TD
  11["Compound Search"];
  5 -->|outfile| 11;
  13["Remove duplicated molecules"];
  5 -->|outfile| 13;
  19["Remove counterions and fragments"];
  13 -->|outfile| 19;
  2["Online data"];
  29["Filter"];
  19 -->|outfile| 29;
  30["Compound Convert"];
  19 -->|outfile| 30;
  31["Molecules to Fingerprints"];
  19 -->|outfile| 31;
  39["Natural Product"];
  29 -->|outfile| 39;
  40["Molecules to Fingerprints"];
  29 -->|outfile| 40;
  44["NxN Clustering"];
  40 -->|outfile| 44;
  5["Change Title"];
  2 -->|output| 5;

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
6 52ea0ed9e 2020-02-19 10:27:06 editing the workflow using the workflow editor
5 d681f0586 2020-01-16 09:16:44 disabled workflow with testtools
4 eb4d724e0 2020-01-15 10:41:35 Workflow renaming
3 7da80b341 2020-01-10 14:56:15 Workflows fix
2 faf6d298a 2019-12-12 13:02:33 unflatten workflows
1 aa2ef61fb 2019-06-12 14:35:10 initial cheminformatics commit

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/cheminformatics/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