[jmchil...@gmail.com]
> Sent: Tuesday, July 22, 2014 4:06 PM
> To: Beck, Emily A
> Cc: galaxy-...@bx.psu.edu
> Subject: Re: [galaxy-dev] Galaxy error
>
> Hello,
>
> Thanks for the bug report. Is this on the main public server (usegalaxy.org)
> or a local instance a
City, IA 52242
> Lab: (319)335-3430
> --
> *From:* John Chilton [jmchil...@gmail.com]
> *Sent:* Tuesday, July 22, 2014 4:06 PM
> *To:* Beck, Emily A
> *Cc:* galaxy-...@bx.psu.edu
> *Subject:* Re: [galaxy-dev] Galaxy error
>
> Hello,
>
> Thanks for the bug report. Is thi
Hello,
Thanks for the bug report. Is this on the main public server (usegalaxy.org)
or a local instance at the University of Iowa?
-John
On Wed, Jul 16, 2014 at 10:39 AM, Beck, Emily A
wrote:
>
> Hello,
>
> I have repeatedly gotten the following error message when attempting to
> use both the
user
usernameemilybeck
quota_percent 19
total_disk_usage52086193970
nice_total_disk_usage 48.5 GB
email emily-b...@uiowa.edu
is_adminfalse
tags_used
model_class User
id 03f0554e2314759e
source HDACollection(f313d1d65c4ee57e,451)
xhr
readyState 4
respo
Hello,
I have repeatedly gotten the following error message when attempting to use
both the mapping and pileup functions in Galaxy. I am using files that I have
previously used successfully with these functions, and cannot fix it.
Thank you.
~Emily Beck
user
usernameemilybeck
quota
I am running into a problem with coloring of my KEGG image produced. When
loading pathview and running this script in R:
pv.out<-pathview(gene.data=gse16873.d, pathway.id="04110", species="hsa",
out.suffix="gse") you get an image with full coloration. With the same
command in galaxy, the image
Never mind problem solved! Thanks again
On Tue, Apr 29, 2014 at 2:40 PM, Bradley Belfiore wrote:
> Thank you for your patience and help, I removed the periods and am running
> into this error:
>
> /bin/sh: /Users/bbelfio1/galaxy-dist/database/files/000/dataset_25.dat:
> Permission denied
>
> Do
Thank you for your patience and help, I removed the periods and am running
into this error:
/bin/sh: /Users/bbelfio1/galaxy-dist/database/files/000/dataset_25.dat:
Permission denied
Does it have to do with the fact Im using SQLite and not Postgres?
On Tue, Apr 29, 2014 at 1:13 PM, Daniel Blanke
FWIW: looks like a trivial xml syntax error is in this line:
interpreter="Rscript">
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R
$gene.data $pathway.id $species $out.suffix $output
.*..*
There seem to be one too many ">" - the first one is pr
Hi Bradley,
For your inputs, don’t use periods (‘.’) within the param names.
Thanks for using Galaxy,
Dan
On Apr 29, 2014, at 12:32 PM, Bradley Belfiore wrote:
> The XML file is:
>
> Pathview is a tool set for pathway based data integration
> and visualization. It maps and renders a wide
Upon going back over my script I got it working on the command line as
suggested, and when attempting to execute in my instance of galaxy I got
this error message which I was not sure about:
Traceback (most recent call last):
File "/Users/bbelfio1/galaxy-dist/lib/galaxy/jobs/runners/__init__.py
The XML file is:
Pathview is a tool set for pathway based data integration
and visualization. It maps and renders a wide variety of biological data on
relevant pathway graphs.
interpreter="Rscript">
/Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $gene.data
$pathway.id$species $out.suffix
Hi Brad
To me, this looks like an error in tool definition file (ie the xml
file). Something like using $gene in the "command" tag without defining
it in a "param" tag. But it is difficult to guess without seeing to full
xml file.
Regards Hans-Rudolf
On 04/29/2014 06:13 PM, Bradley Belfior
So upon doing what you suggested, I get:
bravo:galaxy-dist bbelfio1$ 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
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
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-
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 $gened
Hi Brad
I don't you are using R to execute your R script
How do you call your R script, ie how does the command tag looks in the
tool definition file?
Also, why do you have a "#!/bin/bash" at the beginning of your R script?
Regards, Hans-Rudolf
On 04/27/2014 09:50 PM, Bradley Belfior
I am new to galaxy and while trying to convert an R tool to a Galaxy usable
tool I keep getting: /Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R:
line 1: syntax error near unexpected token `('
/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1:
`args=(commandArgs(TRUE))'
any h
Hi Bassam,
I think that your best bet is to explore this command usage in general,
since this is really a unix question and no detail about how you used
this in Galaxy was provided for others to comment on. I am assuming that
you already checked your Galaxy process and found out if it already
Hi Bassam,
First, I am going to post your question to the galaxy-...@bx.psu.edu
mailing list. This is where local and cloud install Galaxy questions can
get the best exposure to the development community.
Next, this isn't necessarily an error. And was the full line really this?
nohup: ignori
On Wed, Sep 12, 2012 at 12:16 AM, Kenneth R. Auerbach
wrote:
> Hello,
>
> Can anyone tell me why I keep getting this error when I try to do a blast
> search in Galaxy? I checked that the nr database file was there and had the
> right permissions. Does this error mean that Galaxy can't find the nr
Hello,
Can anyone tell me why I keep getting this error when I try to do a blast
search in Galaxy? I checked that the nr database file was there and had the
right permissions. Does this error mean that Galaxy can't find the nr file or
does it mean something else?
An error occurre
Please remember to CC the mailing list.
On Tue, Sep 11, 2012 at 3:37 PM, wrote:
> Hi Peter,
>
>
>
> This is what I get:
>
>
>
> [auerbach@babar ~]$ ls
> /9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr*
>
> /9720/genome_references/ncbi/nr-protein-db/nr-newstyle/nr
>
> /9720/genome_refer
On Tue, Sep 11, 2012 at 3:11 PM, wrote:
> Hello,
>
>
>
> Can any one please tell me what could be causing this error message when I
> try to submit a blast job to Galaxy?
>
>
> An error occurred running this job:BLAST Database error: No alias or index
> file found for protein database
> [/9720/ge
Hello,
Can any one please tell me what could be causing this error message when I try
to submit a blast job to Galaxy?
An error occurred running this job:BLAST Database error: No alias or index file
found for protein database
[/9720/genome_references/ncbi/nr-protein-db/nr-newsty
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