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 thedocker-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.