April 2014 - galaxy-dev - lists.galaxyproject.org

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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tool form in remote mode
by Yanbo Ye 28 Apr '14

28 Apr '14

Hi, Galaxy Developers, I'm trying to integrate galaxy into another system and using its remote mode. While I still want to use the html of the tool form generated by galaxy. I know that I cannot get the html through the API. So I want to write some code to call the tool package code directly. But I can't find the documentation about the tool package and don't know where to start with. Can any one help me? Any help will be appreciated! Best, Yanbo

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user account
by Jun Fan 26 Apr '14

26 Apr '14

Hi everyone I followed the instruction at https://wiki.galaxyproject.org/Admin/UserAccounts to add email verification. I am using GMAIL SMTP server to send out the verification emails. Everything seems fine. If using one of the banned email, an error is there. After register, a verification email is successfully sent out and the page does say that without verification, no job and upload can be done. However when I tried, I CAN upload files and run jobs. The grace period is set to be 0. From the comment, I assume that there is no grace period at all which means no user activity can be carried out. Could anyone point out what I have done wrongly? The by-product of above test is that I need to delete the user I created for test. I searched the dev mail list. The most recent one concerning this is the one sent by Nate in Nov 2011. I just could not find the py file he mentioned, probably that email is too old. I have done a grep search for "operations.append" and "item.deleted" and found two files requests_admin.py and requests.py under lib/galaxy/webapps/galaxy/controllers/. But they are not commented which means that I cannot uncomment them to make "delete user" function available in the UI as Nate suggested. Any guidance? Best regards! Jun

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how to edit the workflow (the connection between Select Variants and SnpEff)
by Wang, Xiaofei 25 Apr '14

25 Apr '14

Dear there, I tried to edit the CloudMap EMS workflow based on my own data. But I failed to make a connection between "Select Variants" and "SnpEff". In fact, I failed to reconstruct the connection between them even when I removed the original one by clicking "x" when moved cursor on the line. The arrow on left of SnpEff does not become green when I drugged the line from output_vcf(vcf) to it after I moved the original one. Could you tell me why does this happen and how should I figure this out? [cid:d1b6886a-ce80-e25c-2ede-e7afbe43263c] Thanks a lot! Best Xiaofei

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