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:
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
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
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
nicholas.robin...@nofima.no wrote:
Hi,
1. INPUT
I am trying to make a simple tool that sends a command to run crimap without
a wrapper ie.
.
command
crimap $param_file $option gt;$output1
/command
..
However,
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 ra...@uga.edu 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
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
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 simple 5
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:
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
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
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
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
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. I
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 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
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
315, in
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,
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
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
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
On Fri, Jun 8, 2012 at 3:27 PM, Greg Von Kuster g...@bx.psu.edu 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
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