Galaxy Resources

Useful links and resources for navigating our Galaxy sysems.

Server Names
vesta.cac.cornell.edu	PEGR	Production Server
hyperion.cac.cornell.edu	Galaxy	Production Server
hestia.cac.cornell.edu	PEGR	Development Server
shrike.cac.cornell.edu	Galaxy	Development Server

danger

Please test your code on the development servers. Do not mess with the production servers!

Navigating of Galaxy-related repos

• EpiGenomicsCode/ansible-egcGalaxy - Ansible-ized Galaxy server deployment (generally this is more of Will’s problem than ours)
  • ephemeris_tools/workflows I believe is where we keep the official pipeline .ga files used in the lab core pipeline. You might see workflows scattered across these other repos but this should be the correct one.
  • ephemeris_tools/ephemeris_tools lists out tools for the core pipeline that we import from the ToolShed
• CEGRcode/ChIP_general-galaxy_tools - Galaxy tools that we custom wrapped for the pipelines (ones that weren’t already in the toolshed)
• CEGRcode/pegr-galaxy_tools - Galaxy tools (XML wrappers of python scripts) that communicate with PEGR by sending POST requests following the execution of a pipeline step so PEGR can display a status update (Green box) and any statistics or figures for the report
• CEGRcode/scriptmanager - Under the galaxy/wrappers directory you can find Galaxy wrappers for the various ScriptManager tools

Linkouts to Galaxy Training and Docs

• Galaxy Server administration highlights:
  • "Ansible" and "Galaxy Installation with Ansible"
  • "Galaxy Tool Management with Ephemeris"