Data management in Medicinal Chemistry workflow

computational-chemistry-med-chem-data/data-management-in-medicinal-chemistry-workflow

Author(s)
Julia Jakiela
Version
1
Last updated
Jan 8, 2024
License
CC-BY-4.0
Tags

Features
Tutorial
Data management in Medicinal Chemistry
Workflow Testing
Tests: ✅
Results: Not yet automated
FAIRness PURL
https://gxy.io/GTN:W00038
RO-Crate logo with flask Download Workflow RO-Crate Workflowhub cloud with gears logo View on (Dev) WorkflowHub
Launch in Tutorial Mode
Download 
output
output
output
output
outfile
outfile
outfile
outfile
ℹ️ Input Dataset
Benzenesulfonyl chloride
ℹ️ Input Dataset
Ethylamine
Compound conversion
Search ChEMBL database
Search ChEMBL database
Compound conversion
Reaction maker
Visualisation
Drug-likeness
Output
Benzenesulfonyl chloride SDF
Output
Substructures from ChEMBL database
Output
Lipinski substructures from ChEMBL database
Output
Ethylamine SDF
Output
Reaction product
Output
Reaction maker logfile
Output
Visualisation of reaction product
Output
Drug-likeness of product molecule

Inputs

Input Label
Input dataset Benzenesulfonyl chloride
Input dataset Ethylamine

Outputs

From Output Label
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0 Compound conversion
toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4 Search ChEMBL database
toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4 Search ChEMBL database
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0 Compound conversion
toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_rxn_maker/ctb_im_rxn_maker/1.1.4+galaxy0 Reaction maker
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy0 Visualisation
toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0 Drug-likeness

Tools

Tool Links
toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl/0.10.1+galaxy4 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_rxn_maker/ctb_im_rxn_maker/1.1.4+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction/3.1.1+galaxy0 View in ToolShed
toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed/2021.03.4+galaxy0 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
  1. Click on Workflows in the Galaxy activity bar (on the left side of the screen, or in the top menu bar of older Galaxy instances). You will see a list of all your workflows
  2. Click on Import at the top-right of the screen
  3. 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”
  4. 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 76375aa18 2024-01-01 19:56:34 workflow tests

For Admins

Installing the workflow tools

wget https://training.galaxyproject.org/training-material/topics/computational-chemistry/tutorials/med-chem-data/workflows/Data-management-in-Medicinal-Chemistry-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