Re: [galaxy-dev] configuring job runner for toolshed tools

2012-07-23 Thread David Hoover
OK, forget what I said earlier. I was watching for a different toolshed tool than what I reconfigured. Never mind, using the guid (the long tool_id shown as an example below) worked correctly. The job was pushed out to the cluster and finished normally. Sorry about the fuss. David On Jul 2

Re: [galaxy-dev] Multiple .CEL file import for microarray analysis

2012-07-23 Thread Ross
Hi, Jon. You're right, there is no cel file management and that's one of many warts needing fixing - it's not a lot of work to make a new tool to create an eSet from a tarball of cel files as you suggest. Unfortunately the rexpression toolkit will soon be deprecated and disappear from the default d

[galaxy-dev] Multiple .CEL file import for microarray analysis

2012-07-23 Thread Jon Manning
Hi all, My apologies if this seems obvious to many of you (seems like something that will have been dealt with)- but I've been rooting around in the docs and mailing list to no concrete avail. I'm looking to Galaxyise our existing (somewhat informal) microarray analysis workflows. I've found

Re: [galaxy-dev] Sample tracking data transfer hangs "in queue" forever

2012-07-23 Thread Luobin Yang
Hi, Greg, I tested your fix in changeset 7388:28b3364341b6, it works fine on my local copy of Galaxy. I am able to transfer, delete, and rename sample datasets without any error message. Thanks, Luobin On Fri, Jul 13, 2012 at 8:19 AM, Greg Von Kuster wrote: > Hello Luobin, > > Your information

[galaxy-dev] Setup questions: data locations, MySQL, and cores

2012-07-23 Thread Steven Peckins
I've been asked to set up a local Galaxy installation specifically for large datasets (tens of terabytes). Is there a list of default locations where Galaxy puts data? As an admin, that would be my first question, but it's not obvious from the documentation, and for large datasets, it's impo