- galaxy-dev - lists.galaxyproject.org

XNAT and Galaxy.
by Neil.Burdett＠csiro.au 13 Jan '13

13 Jan '13

Hi Does anyone have any experience / tools that allow Galaxy to work with a archiving/storage platform such as XNAT? Or maybe point me in the right direction to search, as I believe both platforms are using the REST API Neil

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Galaxy January 11, 2013 Distribution & News Brief
by Jennifer Jackson 11 Jan '13

11 Jan '13

*Galaxy January 11, 2013 Distribution & News Brief* <http://wiki.galaxyproject.org/News/2013_01_11_DistributionNewsBrief> * Complete News Brief <http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11>* * Highlights:* * /*GCC2013 Training Day Topic Nomination closes TODAY!*/ Read more... <http://wiki.galaxyproject.org/News/GCC2013TrainingDayNominations> or see http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay * XML defined Tool shed repository dependencies <http://wiki.galaxyproject.org/DefiningRepositoryDependencies> introduced * Various enhancements <http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11#Other_Tool_Shed> to Tool Shed <http://wiki.galaxyproject.org/Tool%20Shed> containers, display of README files and SVG images, and the tool shed's functional test framework <http://wiki.galaxyproject.org/HostingALocalToolShed#Functional_test_framewo…>. * New genomes <http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11#Data> added to *Main <http://wiki.galaxyproject.org/Main>* Galaxy instance and rsync download. * Plus bug fixes and related enhancements for visualizations, histories, workflows, and tools. * http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org* new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r a4113cc1cb5e / *Thanks for using Galaxy,* / The Galaxy Team <http://wiki.galaxyproject.org/Galaxy%20Team> -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org

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Re: [galaxy-dev] [galaxy-bugs] galaxy.genenetwork.org
by Lei Yan 11 Jan '13

11 Jan '13

Dear Dannon and James, On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker <dannonbaker(a)me.com> wrote: > > • I installed a Cloud Galaxy instance one month ago, and a user > reported that it still has some problems. At that time, I found that it can > be upgraded to new version in the administration page, so I did so. But its > log showed that it “has error”, and the service cannot start. I then tried > to reboot the machine, but Galaxy still could not start and the service is > not responding. > > Can you share the cloud log? This would be the best place to look to find > out what the errors are. > For this Cloud Galaxy instance, I can boot it, but the Galaxy service could not start. So I logged in this server by SSH to get the log files from file system. And I found a strange thing, this server doesn’t mount the three partitions of Galaxy (/dev/xvdg1, /dev/xvdg2, /dev/xvdg3) automatically when booting. I thought this should be automatically, so need I setup something for mounting automatically? I attached the log files, and they are compressed to a zip file “1.log.zip”. > > > • Then I tried to build a new Cloud Galaxy, but after trying at > least 8 times it still didn’t work. Each time, after I launched the Cloud > Galaxy instance, even its State is "running" and the "Status Checks" is > "2/2 checks passed”, but it would still not respond if I opened “http:// > ******.amazonaws.com/cloud”; I never even get to "Welcome to Galaxy on > the cloud". > > Can you share any more information about this? Can you confirm that > you're using the supported AMI, have launched with the correct security > groups, etc? For future reference, just using usegalaxy.org/cloudlaunchis probably the easiest way to make sure you avoid any launch issues. Are > you able to SSH in to the instance? > I am using ami-78a00411. I attached three other files, and they are the AMI I am using, the security groups I am using, and the instance configurations. I never used this usegalaxy.org/cloudlaunch. But it looks good, and I will try this later. Yes, I can login this instance by SSH. But I never even get to "Welcome to Galaxy on the cloud". > > > > Could you please give us some suggestions or let us know who we should > contact about this issue? > > Sending email directly to galaxy-bugs, as you have, for stuff you'd rather > not share with the wider community is the best bet. For anything that > isn't sensitive, emailing galaxy-dev is useful if you're working with > customized or local/cloud installs. > > > I cannot find any telephone number on the Galaxy community pages, and it > would be better if I could talk to someone about the problem over the phone. > > Would it be helpful to chat over IRC and debug this? See the "IRC > Channel" information on http://wiki.galaxyproject.org/Get%20Involved. > > -Dannon Thanks so much for your help. Lei Yan leiyan2000(a)gmail.com UTHSC

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Re: [galaxy-dev] Blank local reference - even after following NGS
by Jorge Sepulveda 11 Jan '13

11 Jan '13

I got it! Stupid mistake of relying on the editor to add tabs to the > hg19 hg19 hg19 ~/ngs/refgenomes/hg19/bwa_indexed/hg19 statement, while it was replacing each tab with 4 spaces. Now all is working fine! > ------------------------------ > > Message: 13 > Date: Wed, 9 Jan 2013 14:31:52 -0500 > From: Jorge Sepulveda <jls2282(a)columbia.edu> > To: galaxy-dev(a)lists.bx.psu.edu > Subject: [galaxy-dev] Blank local reference - even after following NGS > installation instructions > Message-ID: <8AB4A885-98C8-4D44-B51F-CFCD2BD56662(a)columbia.edu> > Content-Type: text/plain; charset=us-ascii > > Hi, > > I set up a local galaxy in my MacPro on 1/3/2013 using: > hg clone https://bitbucket.org/galaxy/galaxy-dist/ > > into this directory: > ~/ngs/applications/galaxy-dist > > Indexed hg19.fa using bwa index to ~/ngs/refgenomes/hg19/bwa_indexed/ > -rw-r--r-- 1 JS staff 6597 Jan 2 15:03 hg19.fa.amb > -rw-r--r-- 1 JS staff 6844 Jan 2 15:03 hg19.fa.ann > -rw-r--r-- 1 JS staff 3101804844 Jan 2 15:02 hg19.fa.bwt > -rw-r--r-- 1 JS staff 775451186 Jan 2 15:03 hg19.fa.pac > -rw-r--r-- 1 JS staff 1550902424 Jan 2 15:06 hg19.fa.sa > > Added: > hg19 hg19 hg19 ~/ngs/refgenomes/hg19/bwa_indexed/hg19 > to this file: > ~/ngs/applications/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/tool-data/bwa_index.loc > > BWA shows up on the galaxy tools list, but the local reference genome box remains empty. It runs fine when I use a reference sequence (chr22.fa) from history. > > If I download bwa (or bowtie2) and install according to the steps in http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup I have the same problem (empty local reference). > > What am I missing? > > Jorge Sepulveda, MD, PhD > Associate Director for Laboratory Medicine, > Medical Director of Laboratory Informatics, > Columbia University Medical Center > Associate Professor, > Department of Pathology & Cell Biology > Columbia University College of Physicians and Surgeons > PH1590B > 622 W 168 St > New York, NY 10032 > Cell: (917) 862-6050 > Office: 212-305-6360 > E-mail:jls2282@columbia.edu > > >

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number of jobs waiting
by Jordi Vaquero 11 Jan '13

11 Jan '13

Hello, I am trying to get an estimated time of job execution. For this reason I need to get the number of jobs waiting in the queue. There is any api I could use ( external to galaxy) in order to check the galaxy queue and get the number of jobs waiting to be executed? I have been looking for this information but I didn't find anything clear. Thanks for your help Jordi

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workflow loading error in galaxy cloudman
by Sun, Wenping [USA] 11 Jan '13

11 Jan '13

Dear Galaxy group, I am uploading the double-ended NGS workflow (Galaxy-Workflow-mt_analysis_0.01_strand-specific_(fastq_double).ga from galaxy website) to galaxy cloudman and had the following error -- Workflow mt analysis 0.01 strand-specific (fastq double) (imported from uploaded file) imported successfully. The workflow requires the following tools that are not available in this Galaxy instance.You can likely install the required tools from one of the Galaxy tool sheds listed below. Tool name Map with BWA, id bwa_wrapper, version 1.0.3 Galaxy main tool shed<http://toolshed.g2.bx.psu.edu/repository/find_tools?galaxy_url=http://50.19…,> Galaxy test tool shed<http://testtoolshed.g2.bx.psu.edu/repository/find_tools?galaxy_url=http://5…,> And when I tried to edit the workflow, it takes forever to load the workflow editor, with "unrecognized Tool: bwa_wrapper" on the background. Does anyone encounter the same problem? I really appreciate your inputs and comments, Kathryn

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Re: [galaxy-dev] Server stops itself
by Rémy Dernat 11 Jan '13

11 Jan '13

Hi Nate, Could you push these patch on the galaxy-dist repository ? Thanks, Regards 2013/1/11 Rémy Dernat <remy.d1(a)gmail.com> > Hi Nate, > > Could you push these patch on the galaxy-dist repository ? > > Thanks, > > Regards >

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Server stops itself
by MONJEAUD 11 Jan '13

11 Jan '13

Hello All, I'm trying to deploy my instance of Galaxy in production. Some tests we've done show that when the number of person connected is high (>20 together), the server stops itself. Sometimes, I have this error in the paster.log: > Exception happened during processing of request from ('127.0.0.1', 60575) > Traceback (most recent call last): > File > "/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line > 1053, in process_request_in_thread > self.finish_request(request, client_address) > File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line > 323, in finish_request > self.RequestHandlerClass(request, client_address, self) > File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line > 641, in __init__ > self.finish() > File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line > 694, in finish > self.wfile.flush() > File "/local/python/2.7-bis/lib/python2.7/socket.py", line 301, in flush > self._sock.sendall(view[write_offset:write_offset+buffer_size]) > error: [Errno 32] Broken pipe Do you have any ideas about this and how resolve it? Cheers!! Cyril -- Cyril Monjeaud Equipe Symbiose / Plate-forme GenOuest Bureau D156 IRISA-INRIA, Campus de Beaulieu 35042 Rennes cedex, France Tél: +33 (0) 2 99 84 74 17

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Re: [galaxy-dev] anybody seen 403s after a recent upgrade?
by Langhorst, Brad 10 Jan '13

10 Jan '13

grr - actually - no it's not fixed I didn't see it on a few refreshes, but apparently it was temporary - or I was hallucinating. brad On Jan 9, 2013, at 3:27 PM, Brad Langhorst <Langhorst(a)neb.com> wrote: > Hmmm > I reconsulted the docs and commented these lines. All seems well again after an apache restart. > I had been running like this for a year or more, and only observed problems after the most recent update > > > # RewriteCond %{IS_SUBREQ} ^false$ > # RewriteCond %{LA-U:REMOTE_USER} (.+) > # RewriteRule . - [E=RU:%1] > RequestHeader set REMOTE_USER %{AUTHENTICATE_sAMAccountName}e > > I just cargo culted those in to begin with… I don't really know what they do. > > > Brad > > On Jan 9, 2013, at 1:21 PM, Nate Coraor <nate(a)bx.psu.edu> > wrote: > >> On Jan 7, 2013, at 10:43 PM, Langhorst, Brad wrote: >> >>> galaxy.web.framework WARNING 2013-01-07 22:06:30,044 User logged in as '(null)' externally, but has a cookie as 'langhorst(a)neb.com' invalidating session >>> 10.254.254.86 - - [07/Jan/2013:22:06:30 -0400] "GET /api/histories/4c8cd68e0b9ed4a7 HTTP/1.1" 403 - "http://galaxy.neb.com/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:17.0) Gecko/20100101 Firefox/17.0" >> >> Hi Brad, >> >> Your proxy server appears to no longer be passing the REMOTE_USER header correctly. Did anything change there? >> >> --nate >> >>> >>> i did not observe this before today… but maybe I've screwed things up in my hg fiddling today. >>> Did anybody else see this? >>> >>> manual refreshes work, but automatic ones don't >>> >>> >>> Brad >>> -- >>> Brad Langhorst >>> langhorst(a)neb.com >>> >>> >>> >>> >>> >>> ___________________________________________________________ >>> 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/ >> > > -- > Brad Langhorst > langhorst(a)neb.com > > > > > -- Brad Langhorst langhorst(a)neb.com

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GATK tools / Realigner Target Creator / pb to create java virtual machine
by Sarah Maman 10 Jan '13

10 Jan '13

Hello, When we run "Realigner Target Creator <http://sigenae-workbench.toulouse.inra.fr/galaxy/tool_runner?tool_id=gatk_r…> for use in local realignment" , I have this error : *Dataset 19: Realigner Target Creator on data 5, data 6, and data 4 (GATK intervals)* Tool execution generated the following error message: Could not create the Java virtual machine. The tool produced the following additional output: Epilog : job finished at jeu. janv. 10 14:49:10 CET 2013 So I have addded java -Xmx4G " in realigner_target_creator.xml file but the problem is not solved. Do you have any idea ?? Thanks in advance, Sarah

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