Posted the following a week ago, but no responses... any thoughts
anyone?
Steve
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Steven Platt
Sent: 12 October 2011 10:35
To: galaxy-dev@lists.bx.psu.edu
Subject:
Dear all,
I have recently installed a local galaxy on our servers.
I could succesfully add a blastable database via the blastdb.loc file.
All is working, so no problems regarding that.
My question however is, how can I set user permissions on the use of these
blast databases, or is this not
On Wed, Oct 19, 2011 at 10:24 AM, Jeroen Crappé jeroen.cra...@ugent.be wrote:
Dear all,
I have recently installed a local galaxy on our servers.
I could succesfully add a blastable database via the blastdb.loc file.
All is working, so no problems regarding that.
My question however is, how
On Oct 19, 2011, at 4:33 AM, Peter Cock wrote:
On Wed, Oct 19, 2011 at 10:24 AM, Jeroen Crappé jeroen.cra...@ugent.be
wrote:
Dear all,
I have recently installed a local galaxy on our servers.
I could succesfully add a blastable database via the blastdb.loc file.
All is working, so no
On Wed, Oct 19, 2011 at 1:41 PM, Fields, Christopher J
cjfie...@illinois.edu wrote:
On Oct 19, 2011, at 4:33 AM, Peter Cock wrote:
On Wed, Oct 19, 2011 at 10:24 AM, Jeroen Crappé jeroen.cra...@ugent.be
wrote:
Dear all,
I have recently installed a local galaxy on our servers.
I could
Hi Ilya,
In addition to the ones that you mention, there is also .metadata,
.extra_files_path, .name which can be useful. The input wrapper will allow
access to any of the attributes associated with the DatasetInstance (see class
of this name in lib/galaxy/model/__init__.py), but using these
Hello Shaun,
I am unable to reproduce at Galaxy main http://usegalaxy.org. Are you
still seeing this behavior?
Thanks!
Jen
Galaxy team
On 10/14/11 5:05 AM, SHAUN WEBB wrote:
Hi. I am using the upload tool to enter some test data in the text box
and checking the convert spaces to tabs box.
Thanks Dan,
That's comforting that the GATK tools will be updated - I'm guessing that
you're already properly fixing what I was hacking. I guess I can wait for the
updated version, so it's no biggie if we fix my specific code - but I think
there's a chance the problems I was having might be an
Nate,
I have been trying to figure out how to make the changes you suggested (i.e.
write output files to the job_working_directory) and then move them over to
files but I am having a difficult time navigating the code. If you could point
me in the right direction, that would be helpful. I
On 10/19/11 3:09 AM, Amit Anand a...@tll.org.sg wrote:
Hi,
I have just installed a local instance of galaxy. Though I am not too familiar
with unix, I preferred a local instance because of large amount of data I have
to process. However, I am unable to upload a file more that 2 GB in size,
Hi all,
I am setting up our own galaxy instance here (or trying to). We'd
like to use fastqc, but I have run into a problem implementing it. Any
suggestions would be most welcome, as to what might be wrong.
1. fastqc runs fine outside of galaxy. But when I try the same file
inside
On Oct 19, 2011, at 8:03 AM, Peter Cock wrote:
On Wed, Oct 19, 2011 at 1:41 PM, Fields, Christopher J
cjfie...@illinois.edu wrote:
On Oct 19, 2011, at 4:33 AM, Peter Cock wrote:
On Wed, Oct 19, 2011 at 10:24 AM, Jeroen Crappé jeroen.cra...@ugent.be
wrote:
Dear all,
I have recently
Lukasse, Pieter wrote:
Hi Peter,
Thanks for the reply.
Does anyone know how to execute a specific workflow from the command prompt?
E.g. run the workflow as a job? Then I could perhaps write a workflow wrapper
tool to overcome this shortcoming.
Hi Pieter,
Have a look at
Hey Ilya,
I'm looking at it now, I'll let you know asap (should be tomorrow).
--nate
Chorny, Ilya wrote:
Nate,
I have been trying to figure out how to make the changes you suggested (i.e.
write output files to the job_working_directory) and then move them over to
files but I am having a
Hi Ross,
Thanks for your advice.
Yes, something like this seems logical. However, after I installed
system-wide before, I noticed that galaxy was expecting fastqc in the
'jars' directory. So, I copied the full directory structure over
there. As such, when I look at the directory
I create an upload file button using upload.xml in one of my xml scripts.
param name=file_data type=file size=30 label=File ajax-upload=true
help=TIP: Due to browser limitations, uploading files larger than 2GB is
guaranteed to fail. To upload large files, use the URL method (below) or FTP
Excerpts from Chorny, Ilya's message of 2011-10-19 23:41:28 +:
I create an upload file button using upload.xml in one of my xml scripts.
...
But when I add it to a work flow and try to have it set the parameters at
runtime, the set at runtime options fails. Any ideas why?
There is
I want to upload an experiment specific file from the workflow and bypass
loading it into the history.
-Original Message-
From: James Taylor [mailto:ja...@jamestaylor.org]
Sent: Wednesday, October 19, 2011 4:50 PM
To: Chorny, Ilya
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re:
Excerpts from Chorny, Ilya's message of 2011-10-20 00:08:11 +:
I want to upload an experiment specific file from the workflow and bypass
loading it into the history.
Galaxy doesn't really support this mode of operation. Data upload and
tool/workflow execution are separated so that all
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