[galaxy-dev] survey

2013-12-12 Thread Philippe Moncuquet
Hi, It would be appreciated if you have time to complete this survey. I set up a simple survey and would greatly appreciate if instance admin would take 2 min to complete it. I will publish results here (or maybe to some more relevant place, let me know) at the end of the month. https://fr.surve

Re: [galaxy-dev] galaxy local installation

2013-12-12 Thread Carl Eberhard
Hello, Edgar - thanks for installing Galaxy! Regarding the screenshots: it looks like Galaxy's static css stylesheet isn't being loaded properly. Is this still occurring for you? Do you see anything when you try to go to http://localhost:8080/static/style/base.css in your browser? (You should see

Re: [galaxy-dev] "Skip automated testing of tools in this revision" setting?

2013-12-12 Thread Nicola Soranzo
Hi Greg, thanks for looking at this! Unfortunately still no test results displayed for http://toolshed.g2.bx.psu.edu/view/crs4/blat Best, Nicola Il giorno mar, 10/12/2013 alle 10.43 -0500, Greg Von Kuster ha scritto: > Hello Nicola, > > The main tool shed is running a bit behind the test tool s

Re: [galaxy-dev] toolshed error on cloudman

2013-12-12 Thread Björn Grüning
Hi Karen, that bug was fixed. Can you update your Galaxy installation? Cheers, Bjoern > Hello, > > > I am currently unable to install a number of tools from toolshed to > our cloud instance. Unfortunately, this pops up for quite a few tools > (I am currently trying to install cuffmerge, but

Re: [galaxy-dev] galaxy local installation

2013-12-12 Thread fernandez Edgar
Hello, Thank you very much for the quick answers. There were very useful. Now I hope I'm not bothering you with a couple more questions. I read more thoroughly the documentation for installing a production environment and I was wondering: 1. Is it possible to run the web server through ap

[galaxy-dev] cloudman console error

2013-12-12 Thread Karen Miga
Hello, I am unable to reach my cloudman console. I was trying to reboot the master. The instance is running on AWS console with no error, I just have no way of access the admin console to terminate or figure out the error through cloud launch. Further, I am now unable to launch a new instance.

[galaxy-dev] toolshed error on cloudman

2013-12-12 Thread Karen Miga
Hello, I am currently unable to install a number of tools from toolshed to our cloud instance. Unfortunately, this pops up for quite a few tools (I am currently trying to install cuffmerge, but I see this again and again). Any help would be appreciated! I am seeing the following error: URL: ht

Re: [galaxy-dev] a galaxy of issues; Job output not returned from cluster,drmaa getting wrong LSF job id and job.o files not being found and moving files occurring before upload completes.

2013-12-12 Thread Nate Coraor
Hi Starr, I'd suggest setting 'retry_job_output_collection' in universe_wsgi.ini to some value > 0 (e.g. 5). You may also want to try remounting the filesystem on which your working directories are located with the `-noac` temporarily just to rule out that the problem is related to attribute cach

[galaxy-dev] problems converting large bcf files to vcf

2013-12-12 Thread Berner, Thomas
Hey guys, we have a problem in our local galaxy instance (10392:1ae95b3aa98d release_2013.08.12) using bcftools (Version: 0.1.19-44428cd) from the tool shed to convert our bcf files into vcf. With bcf files less than ~ 3 GB everything works fine, but above that (we have a 13gb bcf file), the jo