[galaxy-dev] millions for rows in galaxy_session

Is there anyway to have galaxy not insert a row in the galaxy_session file for failed logins. Every ping from china seems to generate a row in galaxy_session. We have anonymous login turned off Robert ___ Please keep all replies on the list

Re: [galaxy-dev] error with multi dataset tool run

> yes, I was the only user but I guess it is too fragile for this kind of thing. postgres wasn’t queuing age jobs correctly so I guess I should track down why. > > From: Hans-Rudolf Hotz > Subject: Re: [galaxy-dev] error with multi dataset tool run > Date: September 1, 2014 at 5:54:10 AM PD

Re: [galaxy-dev] directory as an input file

You might be able to do this by accepting a collection of SAM/BAM files as input instead. This is a quite new feature in Galaxy, see: https://wiki.galaxyproject.org/News/2014_06_02_Galaxy_Distribution Peter On Wed, Sep 3, 2014 at 10:00 AM, Philippe Moncuquet wrote: > Hi, > > I am trying to writ

Re: [galaxy-dev] Examples of Galaxy tools in the toolsheds that install and run JAR files properly?

Peter, Pieter and Dave, thank you for the pointers to your tools - they've been extremely helpful! Now I can see how the process is supposed to work. I'm not really sure where mine is going wrong, but maybe someone here will have ideas. So folks, I've had partial success with a repository that i

[galaxy-dev] directory as an input file

Hi, I am trying to write a wrapper for a tool that take a directory containing SAM/BAM files as an input. I am not sure how to do that, is there another tool that implements this and that I can have a look at ? Any suggestions would be greatly appreciated. Regards, Philip

[galaxy-dev] Proposal: Create a public archive of the GalaxyProject IRC Channel

Hello all, We would like to change the logging policy for the #galaxyproject IRC channel : - *Starting later this fall, the #galaxyproject IRC channel will be logged onlin

Re: [galaxy-dev] Retrieving json files

Thanks Carl, I am using a slightly modified version with "base": https://github.com/saketkc/galaxy_tools/blob/master/visualisation_plugins/inchlib/templates/inchlib.mako#L31 Saket On 2 September 2014 06:09, Carl Eberhard wrote: > Hi, Saket > > There's currently no json dataprovider. > > It's st

Re: [galaxy-dev] Retrieving json files

Hi, Saket There's currently no json dataprovider. It's still relatively easy to get a JSON object, though. I'd recommend: 1. Using the 'line' dataprovider 2. Then, joining the strings returned from it (generally, you want all the strings so be careful using the regex, limit, or offset p

Re: [galaxy-dev] API for multi-file upload

Hello Neil, The newer uploader targets the tool's API with in browser JavaScript - so bioblend say targets the same API with its tool client (https://github.com/afgane/bioblend/blob/master/bioblend/galaxy/tools/__init__.py#L104). I imagine you could get a similar degree of parallelism by splitti

Re: [galaxy-dev] Error with functional tests on cluster

This looks like some script is correct locally but not on the cluster. It looks like the script has some error (like are modules available locally but not on the cluster). At any rate this error is being reported on standard error and the script is continuing to run (hence the datasets being writte

Re: [galaxy-dev] "when else" in ? RE: refresh_on_change : is this a valid attribute? Any other ideas/options??

Galaxy's handling of dynamic options has some restrictions for sure outlined here and it is true that conditional test parameters cannot be set at runtime in workflow execution (the workflow form doesn't have the ability to restructure itself based on the conditional the way the tool form does). A

[galaxy-dev] API for multi-file upload

Hi, I really like the multi-file upload tool in the latest version of Galaxy. Is there an API for it so we can send files via a script rather than using the user interface? If so are there any examples? Thanks Neil ___ Please keep all r

Re: [galaxy-dev] Concept for a Galaxy Versioned Fasta Data Retrieval Tool

I would ask that such a tool be designed to work well in a stand-alone mode outside of Galaxy. Cheers, On Sat, Aug 23, 2014 at 4:24 AM, Dooley, Damion wrote: > We are about to implement a fasta database (file) versioning system as a > Galaxy tool. I wanted to get interested people's feedback