- galaxy-dev - lists.galaxyproject.org

Test ToolShed package_samtools_0_1_19 status error?
by Peter Cock 29 Apr '14

29 Apr '14

Hi all, I'm working on a new wrapper for "samtools depad" (which I have been using with MIRA v4 output), now on the Test ToolShed: http://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad The unit tests work for me locally and via TravisCI. The nightly ToolShed tests are failing - something seems to have gone wrong with the samtools dependency ("status Error") event though the samtools package is listed as a successful installation. Odd... Any thoughts? Thanks, Peter -- Automated tool test results Automated test environment *Time tested:* 2014-04-16 05:07:24 *System:* Linux 3.8.0-30-generic *Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy revision:*13078:6f698dec5895 *Galaxy database version:* 118 *Tool shed revision:* 13018:e20408b06d65 *Tool shed database version:* 22 *Tool shed mercurial version:* 2.2.3 Installation errors Tool dependencies TypeNameVersion samtools package 0.1.19 Error This tool dependency's required tool dependency samtools version 0.1.19 has status Error. Successful installations Repository dependencies* - installation of these additional repositories is required* Tool shedNameOwnerChangeset revision testtoolshed.g2.bx.psu.edu package_samtools_0_1_19 iuc 36aa94676939

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disk space error
by Jess Gaunt 29 Apr '14

29 Apr '14

I hope this is the correct place to submit this problem. I'm using Galaxy main and there appears to be an error in the calculation of the disk space I'm using. I was using 7% of the allowed 250GB and then ran a series of jobs that produced files of ~200GB each. I deleted all of those jobs (most of which hadn't started execution), and then went back and deleted each one permanently, and my usage went back down to 7%. I requested a few jobs which should have produced smaller files, and they paused straight after starting. When I checked back, I was suddenly apparently using 597GB of disk space despite the size on disk of each of my histories adding up to <25GB. I've permanently deleted everything created since the initial problems and still my usage is recorded as 597GB. On Trello, there's a bug report that currently running jobs in deleted histories don't stop execution. Possibly my problem is due to the same bug, despite all the tasks being purged and not recoverable. I cannot do anything on Galaxy until my recorded disk space usage dips back under 100%. Can anyone help? Many thanks, Jessica Gaunt

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Re: [galaxy-dev] RE : Error with "get data" function
by Martin Čech 29 Apr '14

29 Apr '14

Hi Noémie, the special characters are probably in the file path, so some of your folders, or your file name or your computer user name may contain these and when our server gets that path he does not like it and throws an error. Like I said, it is a problem on our side but you can get around it by checking these. Martin On Tue, Apr 29, 2014 at 4:08 AM, DELRIEU Noemie < Noemie.DELRIEU(a)gustaveroussy.fr> wrote: > Hello Martin, > > Thanks for your answer ! I have tried cleaning the browser cache and I > have used another browser, but the problem persists... In fact, I clicked > on "get data" and I chose one file in my computer to download. > I didn't use the character "é" in my e mail adress but I take into account > your advice ! > > Best regards, > > Noémie > ------------------------------ > *De :* emulatorer(a)gmail.com [emulatorer(a)gmail.com] de la part de Martin > Čech [marten(a)bx.psu.edu] > *Date d'envoi :* lundi 28 avril 2014 22:18 > *À :* DELRIEU Noemie > *Cc:* galaxy-dev(a)lists.bx.psu.edu > *Objet :* Re: [galaxy-dev] Error with "get data" function > > Hello Noémie Delrieu, > > can you please describe the process in which the error happens? Do you > only click on 'get data' or do you also select from the sublist? Also try > cleaning the browser cache or using Galaxy with other browser to check on > the issue. > > thanks > > Martin > Galaxy Team > > > On Sun, Apr 27, 2014 at 1:18 PM, DELRIEU Noemie < > Noemie.DELRIEU(a)gustaveroussy.fr> wrote: > >> Hello, >> >> I contact you because I need some help with my galaxy account. I can't >> use function"get data" for 3 days. >> This number error appears : >> >> *GURU MEDITATION: #18e5fee395824913a0f27ff2063a0ead* >> >> >> The adress mail noemie.delrieu(a)gustaveroussy.fr is used for log in on >> server. >> >> >> Thank you. >> >> >> Best regards >> *, * >> >> >> Noémie Delrieu >> >> ___________________________________________________________ >> 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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Re: [galaxy-dev] an uploading problem
by Martin Čech 28 Apr '14

28 Apr '14

Hello Dana, your steps look alright, the upload should not be a problem. However the Galaxy Project does not have control over Cistrome Galaxy server to investigate further. Please use their Google Group to ask them the question directly: https://groups.google.com/forum/#!forum/cistrome thank you Martin Cech Galaxy Team On Mon, Apr 28, 2014 at 4:33 PM, Dana Avrahami-Tzfati < danaav(a)mail.med.upenn.edu> wrote: > Hi Martin, > Thanks for replying, > > I'm using the cistrome.org server. I'm choosing the "upload file from > your computer" option from the cistrome toolbox, than I browse my computer > and choose it. the file is about 317MB. I also check the "convert spaces to > tabs" box, although I'm not sure it is necessary. > > Is there a limit to the amount of data you could upload under your > account?,I'm using 1.8GB right now > > Thank you for your help! > Dana > > ----- Original Message ----- > From: "Martin Čech" <marten(a)bx.psu.edu> > To: "Dana Avrahami-Tzfati" <danaav(a)mail.med.upenn.edu> > Cc: "Galaxy Dev" <galaxy-dev(a)bx.psu.edu> > Sent: Monday, April 28, 2014 11:16:11 PM > Subject: Re: [galaxy-dev] an uploading problem > > Hello Dana, > > how big is the file and how exactly are you trying to upload it? (please > describe your steps) > > Are you using usegalaxy.org server? > > Thank you > > Martin > Galaxy Team > > > On Mon, Apr 28, 2014 at 7:10 AM, Dana Avrahami-Tzfati < > danaav(a)mail.med.upenn.edu> wrote: > > > HI, > > I've been trying to upload a bigwig file for at least 2 days now, but it > > doesn't upload (no error message though). > > > > What to do? Would it help to delete some other heavy files? > > > > Thanks > > > > Dana > > > > -- > > Dana Avrahami-Tzfati, Ph.D. > > Postdoctoral Fellow > > Kaestner Lab > > Dept. of Genetics > > Institute of Diabetes, Obesity & Metabolism > > University of Pennsylvania School of Medicine > > Philadelphia > > > > Phone: 484-343-7598 > > Fax: 215-573-2326 > > email: danaav(a)mail.med.upenn.edu > > ___________________________________________________________ > > 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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Error with "get data" function
by DELRIEU Noemie 28 Apr '14

28 Apr '14

Hello, I contact you because I need some help with my galaxy account. I can't use function"get data" for 3 days. This number error appears : GURU MEDITATION: #18e5fee395824913a0f27ff2063a0ead The adress mail noemie.delrieu(a)gustaveroussy.fr is used for log in on server. Thank you. Best regards, Noémie Delrieu

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NGS Analyses in Galaxy
by Joseph Guan Chong Yeoh 28 Apr '14

28 Apr '14

Dear Galaxy team, I could not access the examples at https://usegalaxy.org/u/aun1/p/ngs-analysis-service . After clicking the links, the pop-up window is blank. Thank you. Regards, Joseph ------------ Joseph Yeoh School of Biological and Chemical Sciences Queen Mary University of London

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an uploading problem
by Dana Avrahami-Tzfati 28 Apr '14

28 Apr '14

HI, I've been trying to upload a bigwig file for at least 2 days now, but it doesn't upload (no error message though). What to do? Would it help to delete some other heavy files? Thanks Dana -- Dana Avrahami-Tzfati, Ph.D. Postdoctoral Fellow Kaestner Lab Dept. of Genetics Institute of Diabetes, Obesity & Metabolism University of Pennsylvania School of Medicine Philadelphia Phone: 484-343-7598 Fax: 215-573-2326 email: danaav(a)mail.med.upenn.edu

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Cloudman/Galaxy autoscaling
by Jim McCusker 28 Apr '14

28 Apr '14

What are the exact conditions that will trigger autoscaling in a galaxy/cloudman instance? I'm seeing 100% utilization on the head node but no attempts by cloudman at spinning up new instances. What sort of state is supposed to trigger that? Thanks, Jim

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Galaxy Error Message
by Bradley Belfiore 28 Apr '14

28 Apr '14

I am new to galaxy and while trying to convert an R tool to a Galaxy usable tool I keep getting: /Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1: syntax error near unexpected token `(' /Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1: `args=(commandArgs(TRUE))' any help as to how to remedy this would be greatly appreciated. The first couple lines of my .R file are # #!/bin/bash args<-(commandArgs(TRUE)) Thanks, Brad

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workflow_execute_parameters.py
by Olivia Doppelt-Azeroual 28 Apr '14

28 Apr '14

Dear developpers, I'm trying to launch a small workflow using the api script workflow_execute_parameters.py I have 2 steps: the input data step and a second step which needs a parameter called prefix. The workflow is attached to this email. I get an error on the parameters inputs which asks me to specify information about an 8th step (which does not exist) Is there a test case available to use this script ? Please keep me informed on that. Have a nice day, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur

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