Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?

> Public profile on LinkedIn <http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/> From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Saturday, August 24, 2013 7:39 AM To: Thon de Boer Cc: 'Galaxy-dev Galaxy-dev' Subject: Re: [galaxy-dev] Why does my trackster com

Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?

echo $? > /mnt/ngs/analysis/svcgalaxy/DATATEST/job_working_directory/001/1916/galaxy_1 916.ec Regards, Thon Thon deBoer Ph.D., Bioinformatics Guru California, USA |p: +1 (650) 799-6839 |m: <mailto:thondeb...@me.com> thondeb...@me.com Public profile on <http://

Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?

. Regards, Thon Thon deBoer Ph.D., Bioinformatics Guru California, USA |p: +1 (650) 799-6839 |m: <mailto:thondeb...@me.com> thondeb...@me.com Public profile on <http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/> LinkedIn From: galaxy-dev-boun...@lists.bx.psu.edu [m

Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?

n deBoer Ph.D., Bioinformatics Guru California, USA |p: +1 (650) 799-6839 |m: <mailto:thondeb...@me.com> thondeb...@me.com Public profile on <http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/> LinkedIn From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@l

Re: [galaxy-dev] Why does my trackster complain about not being able to display BED files?

p: +1 (650) 799-6839 |m: <mailto:thondeb...@me.com> thondeb...@me.com Public profile on <http://www.linkedin.com/pub/thon-de-boer/1/1ba/a5b/> LinkedIn From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Thursday, August 22, 2013 11:11 AM To: Anthonius deBoer Cc: sam gu

Re: [galaxy-dev] Jobs remain in queue until restart

I did some more investigation of this issue I do notice that my 4 core, 8 slot VM machine has a load of 32, with only my 4 handler processes running (Plus my web server), but not even getting more than 10% of the CPU each. There seems to be some process in my handlers that takes an incredible

Re: [galaxy-dev] shall us specify which tool run in cluster?

HI Shenwiyn, The definition of regularjobs etc. is there to allow each job to be run under different environment on the cluster. I am actually not using most of those definitions, except for the BWA tool, which I want to run using 4 slots on our cluster so I use the destination "multicorejobs4

Re: [galaxy-dev] Is there a way through the API to know when a file has completed the upload process?

It seems that there are not a lot of people using/know about the API since all my questions about the API here go unanswered, but I am happy to report that I don't actually need to know if the upload has finished, since it seems you can start a workflow with a dataset that is still being uploaded.Y

Re: [galaxy-dev] Submitting jobs as a real user without using chown, please

oup of trustworthy users, this is a passable way to allow jobs to be submitted as real users.. Thon -Original Message- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Thon de Boer Sent: Thursday, February 21, 2013 11:08 PM To: '

Re: [galaxy-dev] Submitting jobs as a real user without using chown, please

Feb 20, 2013, at 05:52 AM, Nate Coraor wrote: >> >>> On Feb 19, 2013, at 11:02 PM, Thon de Boer wrote: >>> >>> > Hi, >>> > >>> > I am trying to setup my galaxy system to allow jobs to be >>> > submitted as the real user,

[galaxy-dev] Submitting jobs as a real user without using chown, please

Hi, I am trying to setup my galaxy system to allow jobs to be submitted as the real user, since people want to keep an eye on their job on the cluster sometimes and they have no ideas which ones are theirs. I tried the approach on the wiki here: http://wiki.galaxyproject.org/Admin/Confi

Re: [galaxy-dev] History does not automatically update anymore

://localhost:8080$1 [P,L] Before the other /api/ one, the refresh of the history worked again. It seems I need to spend a little more time on this whole proxy setting thing. Thon From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Thon de

Re: [galaxy-dev] History does not automatically update anymore

I do now actually get an error message in my browser saying "Error getting history updates from the server. Internal Server Error" Any ideas? I suspect it is my proxy server settings but not sure. Thon From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.p

[galaxy-dev] Search for toolname from toolshed in workflow editor does not work?

Hi, It seems that the workflow editor does not know how to search for tools that are in the toolshed. The regular toolsearch in the main Analysis window has no problem finding "reorder Sam/BAM" in picard if I search there, but in the workflow editor it seems to only be able to search for tools

Re: [galaxy-dev] Error in database after trying the innocently named, but devastatingly evil "test" in manage_db.sh

-Jan since the current development version of galaxy-dist is broken, but I’m back in business and first order is to create a backup plan Thon From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Thon de Boer Sent: Friday, February 08, 2013 1

Re: [galaxy-dev] Error in database after trying the innocently named, but devastatingly evil "test" in manage_db.sh

(somewhat) OK with having to reload the toolshed tools but I can’t even install or manage any new toolsheds… Thanks Thon From: Daniel Blankenberg [mailto:d...@bx.psu.edu] Sent: Friday, February 08, 2013 12:32 PM To: Thon de Boer Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Er

[galaxy-dev] Error in database after trying the innocently named, but devastatingly evil "test" in manage_db.sh

Hi, I had a small issue with the total usage of my galaxy system showing some negative random number so I figured my database was a little “off”. I snooped around for some database management tools and found “manage_db.sh” which had an option innocently called “test”. I ran it, withou

Re: [galaxy-dev] galaxy api documentation

The documentation for the API is looking real nice...Great... I do have some trouble finding how I move a history item into a data library... Could you give me a few pointers which API call to make for that? We can assume I have the HDA indentifiers for those objects, just need to know the command