[galaxy-dev] IVG display error / local instance of Galaxy
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_disp...@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 --*-- ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Cann't restart server after updating to the latest version
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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cann't restart server after updating to the latest version
Hi Karen, Can you first switch to the user under which Galaxy runs, and go to the home directory of Galaxy: over there, run ./run.sh and watch which error messages appear. This should give you more information. It is recommended after a update to run Galaxy first like this. Kind regards, Joachim Joachim Jacob Contact details: http://www.bits.vib.be/index.php/about/80-team On 06/10/2013 10:33 AM, Karen Chait wrote: 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 ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] a question about profile annotations tool
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___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool shed tool error
Hi Shaun, You should be able to find more details in your Galaxy server's log(s). If you have job separate job handler processes, those logs would be the place to look. --nate On Jun 7, 2013, at 5:31 AM, Shaun Webb wrote: 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. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Installing Galaxy EC2
Hello all, I have a question: does anyone know if it is possible to install Galaxy on an EC2 instance as you would on a local machine, not using CloudMan, and then view it in the web browser by going to public_ip:8080? I have been trying and it has not been working for me. Thanks so much! ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Installing Galaxy EC2
Hi Daniel, This should work fine. You'll need to make sure that you have the host setting in your universe_wsgi.ini like: host = 0.0.0.0 and that the port 8080 is open/accessible in the security group settings for the instance in AWS. Thanks for using Galaxy, Dan On Jun 10, 2013, at 4:42 PM, Daniel Gorelik wrote: Hello all, I have a question: does anyone know if it is possible to install Galaxy on an EC2 instance as you would on a local machine, not using CloudMan, and then view it in the web browser by going to public_ip:8080? I have been trying and it has not been working for me. Thanks so much! ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Fwd: Failed runtime validation of To
Hey all, I've been trying to run a workflow on Galaxy, which basically attempts to establish a correlation between the Chip-Chip, Polymerase binding and Dnase Hypersensitivity data. The input would be these 3 files, I am initially performing a liftover on the Chip-Chip data to convert from hg18 to hg19 and then using the output to establish the correlation. The following error keeps coming up 'Failed runtime validation of To (An invalid option was selected, please verify)' Can anyone please tell me what this might mean? This came up while attempting to run the following tool Traceback (most recent call last): File /galaxy/home/g2main/galaxy_main/lib/galaxy/jobs/runners/__init__.py, line 121, in prepare_job job_wrapper.prepare() File /galaxy/home/g2main/galaxy_main/lib/galaxy/jobs/__init__.py, line 656, in prepare self.tool.handle_unvalidated_param_values( incoming, self.app ) File /galaxy/home/g2main/galaxy_main/lib/galaxy/tools/__init__.py, line 2343, in handle_unvalidated_param_values self.handle_unvalidated_param_values_helper( self.inputs, input_values, app ) File /galaxy/home/g2main/galaxy_main/lib/galaxy/tools/__init__.py, line 2382, in handle_unvalidated_param_values_helper raise LateValidationError( message ) LateValidationError Any assistance would be highly appreciated!! Thanks -Sameer ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Toolshed tool doesn't exist error after installation from toolshed
Hi all,
Looked for this in the list but couldn't find it. Admittedly I was using
gmail to search the list so I may have missed it - apologies if so.
I have put a very simple tool into a local toolshed (latest version of
toolshed) which just consists of an xml wrapper and a perl script in the
repository. (attached) I want to test it prior to putting it in the main
toolshed..
When I install the tool into my galaxy (latest-stable version) it installs
ok.
I then go to run the tool and it loads the interface quite happily but upon
execute it says tool doesn't exist.
I think its looking in the wrong folder on the server for the tool.
In the main galaxy window:
Tool '
galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0'
does not exist, kwd={'tool_state':
u'80025569356339643261396332633035356535356161303366316533393935313439613834366130616239363a3762323235663566373036313637363535663566323233613230333032633230323236343631373436313733363537343232336132303232333233323232376471002e',
'runtool_btn': u'Execute', 'refresh': u'refresh', 'dataset': u'22'}
In the server log:
galaxy.webapps.galaxy.controllers.tool_runner ERROR 2013-06-11 14:23:14,434
index called with tool id '
galaxy-dev.genome.edu.au:9009/repos/slugger/fasta_stats/fasta-stats/1.0.0'
but no such tool exists
128.250.103.244 - - [11/Jun/2013:14:23:14 +1100] POST /tool_runner/index
HTTP/1.1 200 -
https://galaxy-vbc-test.monash.edu/tool_runner?tool_id=galaxy-dev.genome.edu.au%3A9009/repos/slugger/fasta_stats/fasta-stats/1.0.0;
Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/27.0.1453.110 Safari/537.36
The tool is installed in (via the toolshed install process):
shed_tools/
galaxy-dev.genome.edu.au/repos/slugger/fasta_stats/94469f4c8a55/fasta_stats
Any ideas?
Cheers,
Simon Gladman
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