[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
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 $gened
Hi Brad
I don't you are using R to execute your R script
How do you call your R script, ie how does the command tag looks in the
tool definition file?
Also, why do you have a "#!/bin/bash" at the beginning of your R script?
Regards, Hans-Rudolf
On 04/27/2014 09:50 PM, Bradley Belfior
Hi Bassam,
I think that your best bet is to explore this command usage in general,
since this is really a unix question and no detail about how you used
this in Galaxy was provided for others to comment on. I am assuming that
you already checked your Galaxy process and found out if it already
On Wed, Sep 12, 2012 at 12:16 AM, Kenneth R. Auerbach
wrote:
> Hello,
>
> Can anyone tell me why I keep getting this error when I try to do a blast
> search in Galaxy? I checked that the nr database file was there and had the
> right permissions. Does this error mean that Galaxy can't find the nr
Please remember to CC the mailing list.
On Tue, Sep 11, 2012 at 3:37 PM, wrote:
> Hi Peter,
>
>
>
> This is what I get:
>
>
>
> [auerbach@babar ~]$ 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
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