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

[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,

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

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] Error in database after trying the innocently named, but devastatingly evil test in manage_db.sh Hi Thon, The test option runs the upgrade

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

[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] 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

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

[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:

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

PM, Thon de Boer wrote: 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

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

, 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: 'Nate Coraor' Cc: 'Galaxy-dev Galaxy-dev

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

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

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] Why does my trackster complain about not being able to display BED files?

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...@lists.bx.psu.edu] On Behalf Of Thon de Boer Sent: Friday

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 [mailto:galaxy-dev

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 [mailto:galaxy-dev-boun

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

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 complain about not being able to display BED