[galaxy-dev] Amazon cloud setup for galaxy training

Dear, I am setting up with my colleague Jing an Introductory Galaxy training course at the University of Cambridge due to on the 24th September. I am looking for help on how to setup the cloud to have a smooth user experience during the workshop. Would you have any links with information to r

[galaxy-dev] Tool Errors

Hi guys, I am trying to write a tool with a conditional and for whatever reason the results, well aren't any results. It just says 'no seek', which totally bewildering. Does anyone know what this means? Thank you, Calvin my xml file: Classify with Quikr # if $qdb.dbtype == "user" qui

Re: [galaxy-dev] Tool Errors

Hi, as far as I know, it just means your tool did not produced any output, so your results is empty. Nothing more. This is no error, or? The box is not red? Cheers, Bjoern Am 12.09.2014 um 16:28 schrieb Calvin Morrison: Hi guys, I am trying to write a tool with a conditional and for whatev

Re: [galaxy-dev] Tool Errors

Which me thinks is weird, because my code, when given the -v flag will at least put out some info to stdout, or worse case, some errors to stderr, but those are empty too! On 12 September 2014 10:31, Björn Grüning wrote: > Hi, > > as far as I know, it just means your tool did not produced any ou

Re: [galaxy-dev] Tool Errors

You can check the stderr and stdout in the information (small i Icon) site on every dataset. Also can you see what the log is saying? It should provide you the actuall commandline call, which is produced by the wrapper. Cheers, Bjoern Am 12.09.2014 um 16:33 schrieb Calvin Morrison: Which me

Re: [galaxy-dev] Amazon cloud setup for galaxy training

Hello Anne, Overall, what we typically recommend is to launch a new instance and configure it as desired (eg, with tools, histories, and datasets of interest for the workshop). Then share that instance (using the CloudMan share-a-cluster feature -> sm

Re: [galaxy-dev] Tool Errors

The stderr and stdout is empty, according to galaxy. here is paster.log output for quikr when i run it. galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if user == "user" quikr -v -k 0 -s /data/galaxy/galaxy-dist/database/files/000/dataset_103.dat -i /data/galaxy/galaxy-dis

Re: [galaxy-dev] Tool Errors

On 09/12/2014 05:11 PM, Calvin Morrison wrote: The stderr and stdout is empty, according to galaxy. here is paster.log output for quikr when i run it. galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if user == "user" quikr -v -k 0 -s /data/galaxy/galaxy-dist/database/f

Re: [galaxy-dev] Tool Errors

On Fri, Sep 12, 2014 at 4:11 PM, Calvin Morrison wrote: > The stderr and stdout is empty, according to galaxy. > > here is paster.log output for quikr when i run it. > > > galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if user > == "user" quikr -v -k 0 -s > /data/galaxy/gal

Re: [galaxy-dev] Tool Errors

Yes, it seems that has solved the problem! I knew it was something silly. thank you all On 12 September 2014 11:37, Peter Cock wrote: > On Fri, Sep 12, 2014 at 4:11 PM, Calvin Morrison > wrote: > > The stderr and stdout is empty, according to galaxy. > > > > here is paster.log output for quik

Re: [galaxy-dev] Incorrect revision getting referenced in a complex tool dependency - why?

Melissa, The revision recorded in the filesystem path can seem odd at first glance. My inline responses should hopefully clarify that. --Dave B. On 09/10/2014 05:49 PM, Melissa Cline wrote: Hi Folks, Okay, I really need debugging ideas on this one. I have three repositories I'm developi

Re: [galaxy-dev] Incorrect revision getting referenced in a complex tool dependency - why?

Thanks, folks! Everything you've said has clarified many things, and I'm working on putting them into practice. But in the meantime, I've got a new error condition, with the same repositories (and complex repository dependencies), and could use some guidance. I started to see this error conditio

[galaxy-dev] custom datatypes

Hi, I just want a simple data type for my 'custom' datatype (it's just a trained matrix in a specific format generated by my database building tool), so that my tools which use this database will only see ones with that format in the dropdown select list. in my datatypes.xml i have this: then