Hi John,
This is fantastic, thanks for writing this. I've committed the Galaxy-side code in 5050:74048a9ab689, so the patch should no longer be required. I'll try to get something placed on the Cluster page in the wiki, too.
Thanks, --nate
John Chilton wrote:
Hello,
We are looking at integrating some tools into Galaxy for adomain where many of the existing programs are Windows only. My desire is to write tool files and have the certain jobs run remotely on a Windows host (our Galaxy servers are Linux). It wasn't clear how to do this with the existing job runners since they all seem to require a shared file system and absolute file paths that are the same on the Galaxy server as they are on the remote execution hosts.
I developed a new job runner that allows for the remoteexecution of jobs that also rewrites paths and stages files as part of the job execution. There is a server application that needs to be running on the remote machine (*nix or Windows). This application is likely easier to setup/configure than SGE/PBS/etc... because it is a simple Python paste application, with just a few configuration options. There may be valid use cases for this approach for non-Windows applications as well - if you would like a lighter weight server component on the remote system, if shared file systems are impossible/impractical, etc....
The path rewrites are not going to cover every possible way anabsolute path can sneak into the execution, so this is only useful for a subset of tools. But it does handle normal file inputs and outputs, config files, and scripts in the tool definition directory. I welcome input/advice on this approach or the implementation. If there is any way I can improve the code base to the point where it can be included in galaxy-central I would be more than happy to make the desired changes. If not, it is out there for people to use if they have a similar use case.
The server application as well as a patch to add therunner/client to a galaxy-central installation can be found at:
https://bitbucket.org/jmchilton/lwr/src
Thanks for your time, John
John Chilton Software Developer University of Minnesota Supercomputing Institute Office: 612-625-0917 Cell: 612-226-9223 E-Mail: chilton@msi.umn.edu _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev