galaxy-dev June 2013

galaxy-dev@lists.galaxyproject.org

111 participants
189 discussions

Re: [galaxy-dev] Installing Galaxy EC2
by Daniel Gorelik 11 Jun '13

11 Jun '13

Hello, Thanks all, but it it turns out my problem was that the line saying to use the 0.0.0.0 host was commented out.. That was stupid.. Thank you, Daniel On Jun 11, 2013, at 6:46 AM, Quang Trinh <quang.trinh(a)gmail.com> wrote: > Hi Dan and Joachim > You can also try what my students put together, which is based on a config file and more simple. > > https://github.com/modENCODE-DCC/Galaxy/blob/master/docs/README.how.to.laun… > > Thanks, > > Q > > > > > > On Tue, Jun 11, 2013 at 3:30 AM, Joachim Jacob | VIB | <joachim.jacob(a)vib.be> wrote: > Hi Daniel, > > Make also sure you use correct firewall settings ('security groups') in EC2. They are described the Galaxy wiki (http://wiki.galaxyproject.org/CloudMan/AWS/GettingStarted?highlight=%28secu…), but there are some small differences with the setting applied by CloudLaunch (http://dev.list.galaxyproject.org/Cloudman-missing-security-rules-in-wiki-p…) > > Set by CloudLaunch (during my latest launch): > Ports Protocol Source CloudMan > 1-65535 tcp sg-61ba790a > *1-65535 udp sg-61ba790a * > *-1 icmp sg-61ba790a * > 20-21 tcp 0.0.0.0/0 <http://0.0.0.0/0> > 22 tcp 0.0.0.0/0 <http://0.0.0.0/0> > 80 tcp 0.0.0.0/0 <http://0.0.0.0/0> > 30000-30100 tcp 0.0.0.0/0 <http://0.0.0.0/0> > 42284 tcp 0.0.0.0/0 <http://0.0.0.0/0> > > > Cheers, > Joachim > > Joachim Jacob > Contact details: http://www.bits.vib.be/index.php/about/80-team > > > On 06/10/2013 10:54 PM, Daniel Blankenberg wrote: > 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/ > > ___________________________________________________________ > 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/ >

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Toolshed tool doesn't exist error after installation from toolshed
by Simon Gladman 11 Jun '13

11 Jun '13

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.ed…" "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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Galaxy job will stay in waiting under DRMAA runner until manually trigger a command line submission
by Linda Cham 11 Jun '13

11 Jun '13

Hi. Running standalone Galaxy stable_2013.06.03 version on RH6.2 with postgresl db with GPFS filesystem. Setup via the directions in http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster to run all jobs through the LSF DRMAA runner. job_conf.xml: -------------------- <job_conf> <plugins> <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="4"/> </plugins> <handlers> <handler id="main"/> </handlers> <destinations default="lsf"> <destination id="lsf" runner="drmaa"/> </destinations> </job_conf> Scheduler and Galaxy were started. Submit a FASTQ groomer job on a FASTQ file under Galaxy. The groomer job in History will stay in GREY "Job is waiting to run" state until one physically go onto the node and submits a command line job through the scheduler. Once that command line job (e.g. sleep 5) is submitted then the groomer job will show up in the scheduler's job queue and galaxy's HISTORY will now show it as running. I can submit another groomer job after this and it will show up as running. At times, one will see this type of scenario again where one has to manually start a job under the scheduler on the command line to trigger the galaxy's jobs to start running under the scheduler. Is there some setup I am missing in the job_conf.xml above or a flag not set in universe_wsgi.ini? Searching the Galaxy web, I had read that one can set the track_jobs_in_database=True to trigger it to look in memory or database. But that didn't work either. Wonder if anyone seen this type of issue with any runners and have any suggestions on how to debug and fix this. Thanks. Linda

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Failing test in tool shed not shown
by Björn Grüning 11 Jun '13

11 Jun '13

Hi, my augustus repository is shown under the summary page "Latest revision: failing tool tests" but I could not see any failing test in the repository. http://testtoolshed.g2.bx.psu.edu/view/bgruening/augustus Cheers, Björn

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Installing Galaxy EC2
by Daniel Gorelik 11 Jun '13

11 Jun '13

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!

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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!

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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.

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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

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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

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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 --*--

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galaxy-dev June 2013