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
On Mon, Apr 28, 2014 at 4:33 PM, Dana Avrahami-Tzfati <
> 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!
> ----- 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
> 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
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> > http://lists.bx.psu.edu/
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> > http://galaxyproject.org/search/mailinglists/
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.
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.
School of Biological and Chemical Sciences
Queen Mary University of London
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?
Dana Avrahami-Tzfati, Ph.D.
Dept. of Genetics
Institute of Diabetes, Obesity & Metabolism
University of Pennsylvania School of Medicine
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?
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:
any help as to how to remedy this would be greatly appreciated. The first
couple lines of my .R file are
I'm trying to launch a small workflow using the api script
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
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!
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?
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?
Thanks a lot!