Hi, I am trying to access VarCap, as in the paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5316281/. The paper indicates a path and the page is not accepting my account, and if I'll go to usegalaxy page, where I can sing in, this program is not available in search tools. So my question is if this program is installed in galaxy, as mentioned in the paper. Thank you
Each Galaxy server is administered independently. This means that each can contain different tools and shared content (data libraries, histories, workflows) and you will need to create a distinct account on each server in order to use it. This server appears to be publically available and intended as a simplified demonstration of the analysis the publication describes. The authors have more details in the section "A Galaxy instance of VarCap" of the paper.
If you have questions about usage of custom tools or any server issues that may come up while executing the workflow, the authors should be contacted for instructions.
General help for using Galaxy can also be reviewed if you are not yet familiar with using Galaxy (it sounds like you have some experience), but new features/functions are added at each Galaxy release. They are using a Cloudman instance -- and it is not clear which Galaxy version that is based on (you could ask).
- Galaxy Ecosystem: https://galaxyproject.github.io/
- Galaxy Releases: https://docs.galaxyproject.org/en/master/releases/index.html
- Galaxy Tutorials: https://galaxyproject.org/learn/
- Galaxy Support FAQs: https://galaxyproject.org/support/
I didn't find a tool with the name "VarCap" published in the Galaxy Main ToolShed at https://usegalaxy.org/toolshed and it is described as a workflow in the paper implying that other tools are included to perform the complete analysis. Tools not in the ToolShed or not included built-in within the Galaxy distribution will not be available at the Galaxy Main public server at https://usegalaxy.org or the public Galaxy mirror servers: https://galaxyproject.org/galaxy-updates/2018-04/#usegalaxyeu-and-usegalaxyorgau-launched. It may be available at other public Galaxy servers, but you would need to check or ask the authors if they are aware which may also be hosting the tools/workflow (if any): https://galaxyproject.org/public-galaxy-servers/.
Thanks! Jen, Galaxy team