- galaxy-dev - lists.galaxyproject.org

How to Install Bowtie?
by Nicholas Kline 10 Jun '13

10 Jun '13

Hi, Our lab recently installed a local version of Galaxy on Mac OS X 10.8 and can access it at localhost:8080. Now we are trying to install Bowtie version 1 but need help getting it to work. At this point we do not see the tool listed on the left side of the Galaxy menu. Here are the exact steps we followed: 1. create directory /Users/administrator/galaxy-dist/tools_dependencies 2. in universe_wsgi.ini set tool_dependency_dir = tools_dependencies 3. in /etc/paths append /Users/administrator/galaxy-dist/tools_dependencies 4. create tools_dependencies/bowtie/1.0.0/bin 5. create symbolic link tools_dependencies/bowtie/default to directory in step 4 6. download Bowtie, extract it, and copy binaries to tools_dependencies/bowtie/1.0.0/bin Problem: Bowtie is still not appearing in menu on the left side of Galaxy Thanks!

1 0

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 08 Jun '13

08 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 07 Jun '13

07 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 07 Jun '13

07 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