Hi,
Same issue here with multi servers. When I connect to the job manager
instance, I have "This Galaxy instance is not the job manager. If using
multiple servers, please directly access the job manager instance to manage
jobs."
On the web server instance :
Server ErrorURL: http://162.38.181.30:8
Hi,
When I try to use pbs job runners, I get this message in the red box:
Unable to run this job due to a cluster error, please retry it later
And I've got this message in my nohup:
galaxy.jobs.runners.pbs DEBUG 2012-06-08 10:12:12,030 (453) pbs_submit failed,
PBS error 15023: Bad user - no pas
Hi,
There is also another solution if you don't want let users being able to
create libraries.
We have implemented this solution in our local production server here at
Institut Curie.
We add a tool call "local upload file", that takes as entry parameters
the name of the dataset, the type of file a
Hi John,
On Jun 7, 2012, at 11:55 PM, John Chilton wrote:
> I have read through the documentation a couple times, but I still have
> a few questions about the recent tool shed enhancements.
>
> At MSI we have a testing environment and a production environment and
> I want to make sure the tool v
Hi,
1. INPUT
I am trying to make a simple tool that sends a command to run crimap
without a wrapper ie.
.
crimap $param_file $option >$output1
..
However, crimap expects a .par file as input (ie. $param_file should be a
.par file). Because of this I get the error:
Hi everyone,
I'm trying to add a tool which generates 2 files, that I will call ".xxx" (a
text file) and ".yyy" (a binary file) . Both files are needed to use the
result of my tool with an other tool I've added.
So I wanted to create a composite datatype , that I will call ".composite",
whose
On Fri, Jun 8, 2012 at 9:15 AM, Nicholas Robinson
wrote:
> Hi,
>
> 1. INPUT
> I am trying to make a simple tool that sends a command to run crimap without
> a wrapper ie.
> .
>
> crimap $param_file $option >$output1
>
> ..
>
> However, crimap expects a .par file as inpu
Hello,
I am interested in this "local upload file" tool. Can you please send
the files to me as well.
Thanks.
-Raj
On 6/8/12 4:36 AM, Alban Lermine wrote:
Hi,
There is also another solution if you don't want let users being able
to create libraries.
We have implemented this solution in our
On Fri, Jun 8, 2012 at 2:38 PM, Raj Ayyampalayam wrote:
> Hello,
>
> I am interested in this "local upload file" tool. Can you please send the
> files to me as well.
>
> Thanks.
> -Raj
This seems a potentially very useful tool, so putting it on the Galaxy Tool
Shed seems like a better idea (with
Hi all,
Despite the possible security failure, I push the upload_local_tool in
main toolshed under the "data source" repository.
I notice about the possible security failure and the way to fix it.
I also have a simple 5 minutes method to modify existing tools to allow
users to choose the directo
Re,
My bad: upload_local_tool -> upload_local_file tool
Bests,
Alban
> Hi all,
>
> Despite the possible security failure, I push the upload_local_tool in
> main toolshed under the "data source" repository.
>
> I notice about the possible security failure and the way to fix it.
>
> I also have a
Hi Greg,
thanks! I can confirm that it is working now. I can upload new
datatypes.
What is not working is the update of such tools from the toolshed.
I get the following error.
URL:
http://localhost/toolshed/repository/check_for_updates?galaxy_url=http://localhost/&name=molecule_datatypes&owner=a
Hi Bjoren,
What revision are you seeing this in? I don't think this issues exists in
Galaxy central's tip, but let me know.
Thanks!
Greg
On Jun 8, 2012, at 10:44 AM, Björn Grüning wrote:
> Hi Greg,
>
> thanks! I can confirm that it is working now. I can upload new
> datatypes.
> What is not
On Jun 8, 2012, at 8:42 AM, Peter Cock wrote:
> On Fri, Jun 8, 2012 at 2:38 PM, Raj Ayyampalayam wrote:
>> Hello,
>>
>> I am interested in this "local upload file" tool. Can you please send the
>> files to me as well.
>>
>> Thanks.
>> -Raj
>
> This seems a potentially very useful tool, so putt
I'm trying to add mm10 to a Galaxy instance built using Mercurial on May
31st (using Postgres). I've added the .fa file, prepared bwa, bowtie,
samtool indexes, etc., edited all of the .loc files for individual tools
and restarted the server daemon. mm10 appears in the list of genomes
available fo
Hi Alban,
Yes, we would very much interested in this tool, since our current workaround
is not a desired one (a python mini http server!).
Thank you for sharing it :)
-Mehmet
On Jun 8, 2012, at 4:36 AM, Alban Lermine wrote:
> Hi,
>
> There is also another solution if you don't want let u
Hello Greg,
Thanks for the prompt and detailed response (though it did make me
sad). I think deploying tested, static components and configurations
to production environments and having production environments not
depending on outside services (like the tool shed) should be
considered best practic
On May 30, 2012, at 7:18 PM, Luobin Yang wrote:
> Hi,
>
> I upgraded Galaxy to the latest version using the command: "hg pull -u", then
> when I run "sh run.sh" I got the following error messages:
>
> Initializing openid_conf.xml from openid_conf.xml.sample
> Initializing tool-data/bowtie2_indi
On May 31, 2012, at 11:19 PM, Ann Black-Ziegelbein wrote:
> Hi -
>
> I have been trying to run a quick test using the tool_dependency_dir
> configuration option to prove out how it works ... but unfortunately I can't
> get it to function right. I was hoping someone could point out my error.
On Jun 1, 2012, at 5:31 AM, Sarah Maman wrote:
> Hello Nate,
>
> As agreed at the conference in Lyon, here's a screen printed my instance of
> Galaxy (please look at the end of this mail), but the layout is not exactly
> the same as that seen in the instance of Galaxy on the public server.
Hi
On Jun 4, 2012, at 1:06 AM, Derrick Lin wrote:
> Hi guys,
>
> Today my institute ran a galaxy training with about 20 people. We didn't
> implement multiple instances for galaxy python. When everyone started
> submitting jobs, the thread pool filled up very quickly, soon after the
> galaxy thre
On Jun 4, 2012, at 7:24 AM, Peter Cock wrote:
> Dear all,
>
> Does Galaxy have any mechanisms to set the priority of jobs
> submitted to the cluster? Specifically I am interested in SGE
> via DRMAA, but this is a general issue. If there is some existing
> code, I might be able to use it for the f
On Jun 4, 2012, at 8:58 AM, CHEBBI Mohamed Amine wrote:
>
>
> -- Forwarded message --
> From: CHEBBI Mohamed Amine
> Date: 2012/5/25
> Subject: Proftpd Problem
> To: galaxy-dev@lists.bx.psu.edu
>
>
> Hi,
> I'am trying to set up ProFTP on Debain to enable FTP upload on Galaxy
On Jun 4, 2012, at 11:34 AM, Shantanu Pavgi wrote:
>
> I am getting following errors in the galaxy log:
>
> {{{
> Error reading tool from path: human_genome_variation/sift.xml
> Traceback (most recent call last):
> File "/home/shantanu/galaxy/galaxy-uab/lib/galaxy/tools/__init__.py", line
> 31
Hi Jelle and Sarah,
I can't work on this issue right this moment, but have created an issue to
track so it's not forgotten:
https://bitbucket.org/galaxy/galaxy-central/issue/767/when-remote_user-true-a-lot-of-new-empty
--nate
On Jun 3, 2012, at 7:43 AM, Jelle Scholtalbers wrote:
> Hi Sarah,
>
On Jun 4, 2012, at 4:26 PM, Gallant, Jason wrote:
> Greetings Galaxy Devs!
>
> I've been doing a fair amount of poking around in the forums and on the wiki
> but haven't found a satisfying answer to my query...
>
> Has anyone come up with a workable solution to run jobs from a local
> installa
Hi Nate,
Excellent to hear! I will stay tuned for this most welcome update. In the
meantime, I welcome any other user's input on their solutions :)
Cheers,
Jason
-
Jason Gallant, Ph.D.
Postdoctoral Research Associate
Department of Biology
BRB 224, 5 Cummington Street
Boston University
Bos
Hi John,
On Jun 8, 2012, at 1:22 PM, John Chilton wrote:
> Hello Greg,
>
> Thanks for the prompt and detailed response (though it did make me
> sad). I think deploying tested, static components and configurations
> to production environments and having production environments not
> depending on
On Jun 5, 2012, at 6:08 PM, Dorset, Daniel C wrote:
> I’m trying to troubleshoot why I can’t retrieve output from my Galaxy cluster
> instance. I notice that when I click on any output, the URL is something like:
>
> http://[root galaxy address]/datasets/[some 16-character hash]/display/[file
Thanks Nate! That's very helpful.
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Friday, June 08, 2012 3:31 PM
To: Dorset, Daniel C
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] How does Galaxy access datasets?
On Jun 5, 2012, at 6:08 PM, Dorset, Daniel C
Hi Nate !
Thank-you for your response. I have finally fixed the problem. In fact I
had to add the line above in the /etc/proftpd.modules.conf :
AuthOrder mod_sql.c mod_auth_unix.c
This enables the checking of user login and password from SQL tables.
So Now I can upload data by FTP from my Galaxy s
On Fri, Jun 8, 2012 at 3:27 PM, Greg Von Kuster wrote:
> Hi John,
>
> On Jun 8, 2012, at 1:22 PM, John Chilton wrote:
>
>> Hello Greg,
>>
>> Thanks for the prompt and detailed response (though it did make me
>> sad). I think deploying tested, static components and configurations
>> to production e
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