- galaxy-dev - lists.galaxyproject.org

Tool shed tool error
by Shaun Webb 10 Jun '13

10 Jun '13

Hi, I have created a tool and added it to a local tool shed. It installs ok but when I run the tool I get the following error: "Unable to run job due to a misconfiguration of the Galaxy job running system. Please contact a site administrator." I get the same error with other tools in my tool shed both on our test galaxy site (updated to latest release and using new job_conf.xml file) and our production site (Feb 8th dist). I then loaded the tool to the main glaxy test tool shed and installed from there, I still get the same error. I am now assuming that the problem is with the tool. The error is rather vague, can anyone point me to what could possibly cause this error? Thanks Shaun Webb University of Edinburgh -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

2 1

a question about "profile annotations" tool
by Shu-Yi Su 10 Jun '13

10 Jun '13

Hi, I have a question about the tool "Profile Annotations" in the Operate on Genomic Intervals. I am trying to install this tool on the galaxy, but when I run the program, it shows this error message: AssertionError: Configuration error: Table directory is missing (/g/funcgen/galaxy/tool-data/annotation_profiler/dm3) What files should I provide in /g/funcgen/galaxy/tool-data/annotation_profiler/dm3 ? Does any one knows where i can download the annotation profiles or how I generate them? Thank you very much for your attention. Best regards, Shu-Yi

1 0

Cann't restart server after updating to the latest version
by Karen Chait 10 Jun '13

10 Jun '13

Hello, I upgraded to the latest version running: hg pull and then hg update. When trying to stop and start galaxy I got the following message: $ galaxy stop Stopping galaxy... No PID file exists in paster.pid done. $ galaxy start Starting galaxy... Entering daemon mode ...done. But the galaxy status remains 'stopped'. Same happens when running restart to the server. Do you know what is the problem and how to overcome it? Thanks Karen

2 1

IVG display error / local instance of Galaxy
by Sarah Maman 10 Jun '13

10 Jun '13

Hello, I try to connect my local instance of Galaxy to IGV but I receive this error message : *server redirected too many times (20)* I can see the IGV link in my dataset and I can open IGV thought my local instance but my dataset is not found. Here is modifiactions of my local instance: * My httpd.conf file has the location match added : | <LocationMatch ^/galaxy/display_application/[a-zA-Z0-9]+/igv.*>| | RequestHeader set REMOTE_USER igv_display(a)toulouse.inra.fr| | Satisfy Any| | Order deny,allow| | Allow from all| | </LocationMatch>| * IGV is setted up as a display application in my local instance: |<display file="igv/bam.xml" /> |* I new RewriteRule is now added in my httpd.conf file : RewriteRule ^/galaxy/display_application/[a-zA-Z0-9]+/igv_bam/web_link_main/[a-zA-Z0-9]+/data/galaxy_[a-zA-Z0-9]+.bam /path/to/my/galaxy/database/files/$1 [L] | | Do you have any idea ? Could you please help me ? Thanks in advance, Sarah Maman -- --*-- Sarah Maman INRA - LGC - SIGENAE http://www.sigenae.org/ Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53 --*--

1 0

how to access galaxy model in the tool wrapper
by BingXin Lu 09 Jun '13

09 Jun '13

Hi all, Do you know any way to access galaxy model (like 'HistoryDatasetAssociation') in the tool wrapper python file for a newly added tool, without overriding 'exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr)'? Thank you very much. Best Regards, -Bingxin

1 0

disk space usage
by Katie Kathrein 08 Jun '13

08 Jun '13

Hi, I am having an issue with disk space. I had some problems with loading datasets and ended up deleting a few that had errors. Now things are fine, except that my disk space says 90% is being used, yet I only have about 70 GB of data right now. Please help! Thanks! Katie Katie Kathrein, Ph.D. Zon Lab Children's Hospital Boston Karp Research Laboratories, 7005H 1 Blackfan Circle Boston, MA 02115 kkathrein(a)enders.tch.harvard.edu

2 1

Error in getting updates from server
by Mather Ali Khan 08 Jun '13

08 Jun '13

Hi, Two days earlier i have executed my file for tophat, since then it is still in gey color and not getting any updates from server. Should i delete the executed file and run again? Please help me out. Thanks Mather -- *Mather Ali Khan, Ph.D.* *247, Bond Life Sciences Center* *1201 Rollins Street* *University of Missouri-Columbia* *Columbia, MO, 65211, USA * Think Green - don't print this email unless really needed

2 1

Can I use javascript in the xml to select a date on a calender?
by Ramon Tiburski 07 Jun '13

07 Jun '13

Hi, I want to select a date from a calender in my tool, but I think that it's not possible in the xml. I was looking for some examples with xml, javascript and jquery but I could not do what I wanted. My code is: <tool id="idPlot" name="Plot"> <command interpreter="bash">r_wrapper.sh $script_file</command> <inputs> <param name="arg1" type="text" value="" label="Data 1"/> <param name="arg2" type="text" value="" label="Data 2"/> </inputs> <configfiles> <configfile name="script_file"> pv1 = "$arg1" pv2 = "$arg2" pdf("${out_file1}") source("/home/ramao/Galaxy-ES/tools/my_tools/modelo.R") devname=dev.off() </configfile> </configfiles> <outputs> <data format="pdf" name="out_file1"/> </outputs> </tool> I want that when I click in the input area the tool, it shows a calender to me select the date. Is this possible? With javascript? Or what? Thanks

2 2

bug in galaxy-central security
by Robert Baertsch 07 Jun '13

07 Jun '13

James, I upgraded to the latest galaxy-central and starting with a blank database. When I add more than 20 users, the security group admin screen doesn't populate. mako is pulling the correct data but there is some jquery code for autocomplete or search that seems to be having trouble. Here is a screen shot. Let me know if you want admin access to this server and I'll setup a user for you. -Robert

2 6

Basic setup question
by Malcolm Tobias 07 Jun '13

07 Jun '13

All, I manage a cluster and have been asked to set up a local instance of galaxy. I'm neither a galaxy user nor a biologist, so apologies in advance if my terminology is off. I have a basic setup running now, but have been asked to include the option to "display at UCSC Main" when a user uploads a bam and clicks on the dataset. Currently I have the options of "display in IGB Local Web". I've tried this at a few of the other Galaxy sites, and the behavior seems unpredictable. Uploading the same data set to some sites gives me this option, while others don't. I'm assuming this is determined by the option in the universe_wsgi.ini file: # UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt ucsc_display_sites = main,test,archaea,ucla but uncommenting this option and restarting the server doesn't help. Increasing the log_level to DEBUG doesn't provide any insight. Any suggestions about how to proceed? Could there be any firewall-related issues? I ask because of this in the configuration file: # If use_remote_user = True, display application servers will be denied access # to Galaxy and so displaying datasets in these sites will fail. # display_servers contains a list of hostnames which should be allowed to # bypass security to display datasets. Please be aware that there are security # implications if this is allowed. More details (including required changes to # the proxy server config) are available in the Apache proxy documentation on # the wiki. Thanks in advance, Malcolm -- Malcolm Tobias 314.362.1594

2 2