So upon doing what you suggested, I get:
bravo:galaxy-dist bbelfio1$ Rscript
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R
'/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA'
Error in grep(species, pathway.id) :
argument "pathway.id" is missing, with no default
Calls: pathview -> gre
Dear Ido,
Thank you for your response, but I don't have a usage question. I've read
through all of the information on managing datasets and it seems to be a
calculation error on Galaxy. I'm hoping that an admin can recalculate my
disk usage as described here (
https://wiki.galaxyproject.org/Admin/D
Yes when running in command line I get:
bravo:galaxy-dist bbelfio1$ Rscript
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R
Error in value[[3L]](cond) :
failed to read experimental design data: cannot open the connection
Calls: tryCatch -> tryCatchList -> tryCatchOne ->
In addition: W
The initial error now seems to be taken care of and now am getting this
message on attempting to run tool:
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
line 153, in prepare_job
job_wrapper.runner_command_line = self.build_command_line(
job_wrapper, include_metadata=i
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 yo
Noémie:
please try to avoid using the character 'é' in your email address within
Galaxy. Our system is not prepared to handle it yet, we are sorry.
regards
Martin
Galaxy Team
On Mon, Apr 28, 2014 at 4:18 PM, Martin Čech wrote:
> Hello Noémie Delrieu,
>
> can you please describe the process i
One more thing: all the Galaxy screencasts should be also listed on this
page: https://wiki.galaxyproject.org/Learn/Screencasts
M.
On Mon, Apr 28, 2014 at 4:24 PM, Martin Čech wrote:
> Hello Joseph,
>
> these videos seem to be pretty old, nowadays all videos are on Vimeo at
> http://vimeo.com/
Hello Joseph,
these videos seem to be pretty old, nowadays all videos are on Vimeo at
http://vimeo.com/galaxyproject/videos/sort:plays/format:thumbnail
However you can reach the videos on the givent page too: Right click the
link and click 'open in new tab/window'. That should open it and play th
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,
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 <
dan...@mail.med.upenn.edu> wrote:
> HI,
> I've been trying to upl
Ahh, ok. No, that isn't exposed currently, though we've talked about
better autoscaling control before and I can see how it would be valuable.
If this is something you'd want to change in the near term, you could
always run a custom version of cloudman (launching via your own bucket
instead of ou
I was thinking of the job idle time, where we spin up more instances if
jobs sit waiting for, say, 15 seconds instead of 60.
Jim
On Mon, Apr 28, 2014 at 2:05 PM, Dannon Baker wrote:
> The time after which it culls instances? It is not, but because of the
> way Amazon bills for instances, you n
The time after which it culls instances? It is not, but because of the way
Amazon bills for instances, you never want to kill an instance until the
end of the hour (since, regardless of when you kill an instance, you're
billed for the remainder of the hour).
-Dannon
On Fri, Apr 25, 2014 at 3:01
Hi Dave,
This problem persists (or has reoccured),
This tool dependency's required tool dependency samtools version
0.1.19 has status Error.
Did you discover anymore last week? Sorry for the lag in my reply, I busy
with other things.
Thanks,
Peter
On Mon, Apr 21, 2014 at 2:24 PM, Dave Bouvier
Hi Brad
On 04/28/2014 05:26 PM, Bradley Belfiore wrote:
So upon doing what you suggested, I get:
bravo:galaxy-dist bbelfio1$ Rscript
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R
'/Users/bbelfio1/Documents/sample.txt' '04110' 'HSA'
I said "Rscript_wrapper.sh /Users/bbelfio1/galaxy-
Its better to post usage questions at https://biostar.usegalaxy.org/
best,
ido
On Apr 28, 2014, at 2:50 PM, Jess Gaunt wrote:
> 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.
This is not what I suggested, I said
Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
replacing $genedata $pathwayid $species $output with meaningful arguments
On 04/28/2014 04:29 PM, Bradley Belfiore wrote:
Yes when running in
> On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
>>
>> The initial error now seems to be taken care of and now am getting this
>> message on attempting to run tool:
>>
>> File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py",
>> line 153, in prepare_job
>> job_wrapper.runner_
again, have you tried running your Rscript outside of Galaxy called by
Rscript_wrapper.sh ?
To me, it looks like you have a bug in your Rscript and/or your wrapper.
Hans-Rudolf
On 04/28/2014 03:58 PM, Bradley Belfiore wrote:
The initial error now seems to be taken care of and now am getting
On Mon, Apr 28, 2014 at 2:40 PM, Hans-Rudolf Hotz wrote:
> On 04/28/2014 03:32 PM, Bradley Belfiore wrote:
>>
>> Thank you for your quick response, my command tag is:
>>
>> interpreter="bash">Rscript_wrapper.sh
>> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
>> $pathwayid $spec
"Please keep all replies on the list by using "reply all""
well, what happens if you run
Rscript_wrapper.sh
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata
$pathwayid $species $output
on the command line yourself (or rather as the user galaxy is running
as), replacing $gened
Hi Brad
I don't you are using R to execute your R script
How do you call your R script, ie how does the command tag looks in the
tool definition file?
Also, why do you have a "#!/bin/bash" at the beginning of your R script?
Regards, Hans-Rudolf
On 04/27/2014 09:50 PM, Bradley Belfior
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.delr...@gustaveroussy.fr is used for log in on server.
Thank you.
Best regards,
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
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
_
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 Diabete
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 h
Dear Dannon,
when the parameter (that I need to fix) is 'set at runtime', the value
that it gets is: __lt__galaxy.tools.parameters.basic.RuntimeValue
python workflow_execute_parameters.py 43359c833b8977b01d6237d9b839dc27
http://127.0.0.1:8080/api/workflows f2db41e1fa331b3e a799d38679e98
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
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