Galaxy wrappers for SynBio Design Tools

galaxy_selenzyme

Creating a tool within Galaxy to run Selenzyme.

See:

Tutorial to create a Galaxy tool: https://galaxyproject.org/admin/tools/add-tool-tutorial/
How to install it in the Galaxy container: https://github.com/bgruening/docker-galaxy-stable
Example for Uniprot: https://toolshed.g2.bx.psu.edu/repository?repository_id=c8774310981b07c5

Plan:

Create a basic command line tool using Python requests that submits a the reaction SMILES and gets the predicted sequences.
Create a Galaxy Tool XML file.
Check that the Galaxy container has requests installed, otherwise add to the docker-compose file.
Mount the folder with the tool in the container.
Install the tool locally in Galaxy.
Use planemo in order to create a repository in the toolshed.
Register in the toolshed.
Install in the Galaxy container from the toolshed.
Create a tool using Galaxy XML that post JSON request and receives a JSON response (no local tool running in the Galaxy server).
Submit the purely XML tool to the Galaxy Tool Shed.

To learn more about Selenzyme:

Carbonell, Pablo, et al. Selenzyme: enzyme selection tool for pathway design. Bioinformatics 34: 2153-2154, (2018). https://doi.org/10.1093/bioinformatics/bty065

Creating a tool within Galaxy to run OptBioDes (optimal design of experiments).

Plan:

Create a basic command line tool using Python that submits a CSV with the design specifications sheet.
Create a Galaxy Tool XML file.
Use planemo in order to create a repository in the toolshed.
Register in the toolshed.
Install in the Galaxy container from the toolshed.
Write documentiation about the design specifications sheet.

A tool to visualize pathways by querying an RPViz server.

RPViz returns an interactive HTML file that requires javascript. The RPViz tool has to be included in the Galaxy whitelist.