[galaxy-dev] automatic installation of galaxy tools...
Hi all, I am working on a way to add/install tools to galaxy in a more automated way. I need that for the galaxy-taverna interoperability work we are doing (https://trac.nbic.nl/elabfactory/wiki/eGalaxy). The generator produces a galaxy tool (.zip or an .xml + .rb) that I want to install as easily as possible. Since, this is sth that other people might be interested I was thinking of generalising it. The idea is to create a script (background process) where we specify an association between a galaxy tool directory and a galaxy section. Every time something is copied in that directory it will be picked up by the script, which will check if it is a valid tool, and add it to tool_conf.xml in the specified section (+optionally restart the server). I am assuming that people would have already worked on/thought of something similar for their own needs. So, my questions are: a) anyone knows if sth similar already exists and how reusable it is, and b) does it sound like something useful (apparently, to people that manage tools frequently!) Cheers, Kostas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] workflow representation and execution...
Hi Glen, Good to know. I assume that currently that is not happening though, right? If yes, is it in your immediate plans? It should happen now - each step in the workflow would get submitted as a separate job to the cluster. At that point it is up to the job scheduler and not Galaxy to determine where the job is run. Ah, great. So if two connected tasks run on different nodes how is data movement between these nodes handled? Is there a distr. file system used to take care of that or it's being done manually? Thanks you! Kostas ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] workflow representation and execution...
Hi Glen, All is clear now. Thanks for the info! :) K. the job should copy its output files into the Galaxy database/files directory before it terminates. So assuming you are not using data staging and the database directory is shared via NFS, then the next tool will read the files from this location. There is an option to stage files if you use TORQUE, but I think most sites use the network shared storage approach. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
