Hi Rob,
Indeed, I had/have some difficulties with setting temporary
directories. The problem was that FTP uploaded data was first copied to
TMPDIR prior to being put in the database directory.
My solution: I extended the /tmp partition to several GB's, by mounting
a bigger device over it.
Hi Akshay,
I am going to post your question over to the galaxy-...@bx.psu.edu
mailing list, to give it better viability.
You could probably run an sql query against a database table to find out
this information, but there may be a better way. Let's see if someone
has a method worked out
Akshay
If you have galaxy_reports running on your server you can see the most likely
logged in users under: Users/Date of last login when you query it for 0 days.
You at least have a login per day (not on the hour though).
For restarting purposes we ignore viewers and monitor the running jobs in
It works!!
I didn't know I have to save before to use circster!!
Great!!
Thanks a lot!! :D
Stefania
On 27/mar/2013, at 17:57, James Taylor ja...@jamestaylor.org wrote:
I think if you save your trackster visualization first then switching
over to circster should work fine.
--
James Taylor,
On Thu, Mar 28, 2013 at 4:36 AM, Raj Ayyampalayam ra...@uga.edu wrote:
Hello,
I am trying to get the trinity wrapper to work on our local galaxy
installation using the latest trinity version.
The main issue is that the Trinity.pl call has --SS_lib_type None in the
script file. The data I am
Richard,
You can find the code for admin users stopping jobs in
lib/galaxy/web/base/controllers/admin.py, in the jobs method of the
Admin class. Hopefully that will provide the base structure for what you
want to accomplish.
--Dave B.
On 3/27/13 12:02:20.000, Richard Park wrote:
Hey
Hi Assaf,
After all, the problem appears not to be total size of the history, but
the size of the individual datasets.
Now, histories which contain big datasets (1GB) imported from Data
Libraries causes the exporting process to crash. Can somebody confirm
if this is a bug? I uploaded the
OK, it seems to be a proxy error.
When the proxy does not receive data from the server, it times out, and
closes the connection.
I think the process that packs the datasets takes too long, so the
connection is closed before the packaging is finished? Just a gues...
From the httpd logs:
=
On Mar 22, 2013, at 4:57 PM, Lance Parsons wrote:
Nate Coraor wrote:
On Mar 22, 2013, at 11:56 AM, Lance Parsons wrote:
I have been running a Galaxy server for our sequencing researchers for a
while now and it's become increasingly successful. The biggest resource
challenge for us has
Hi Greg,
Is there anything left of the old (pre-hg) Tool Shed? I'm wondering if I ever
uploaded this tool back in early 2011, in which case could it have got lost
in the migration to the current hg-based Tool Shed?:
Hi Peter,
Everything that was in the pre-hg tool shed was moved to the new tool shed - I
don't remember any issues during that transition that would have eliminated
anything. I don't think there is anything retrievable from the original tool
shed at this point without some effort. You most
Hey Alex,
Thanks for the quick response. The reason why I asked this question is because
we reimplemented our plugin WS-Extension tool, which allows users to import web
services as tools in Galaxy. This process involves making changes to
tool_conf.xml, hence the restarting process is required.
Hi,
Today, I found out that one user in our local galaxy installation (the
administrator user) has a negative disk usage.
- Reports shows : -72780720701 bytes
- Galaxy history shows: -1%
Does anybody have suggestions on what might be causing this and how to
solve it?
There is about 660 Gb of
I haven't looked at this directly, but it should be using None, in
which case the correct comparison is library_type is None and
library_type is not None.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Mar 28, 2013 at 6:35 AM, Peter Cock p.j.a.c...@googlemail.com
Hi,
None of the solutions that were mentioned fixed the issue. I will do
some more debugging later this evening.
Thanks,
Raj
On Thursday, March 28, 2013 12:26:56 PM, James Taylor wrote:
I haven't looked at this directly, but it should be using None, in
which case the correct comparison is
Hi Galaxy-Dev,
I have a new local instance that submits to cluster1 via pbs-drmaa-1.0.14.
Galaxy is on a VM that is a submit node on cluster1, and there is a shared
filesystem amongst all the clusters where the datasets are stored. The Galaxy
VM is also a submit node on cluster2 and we have
Has anyone configured SSL for nginx on CloudMan (AWS)? If so, can you share
your nginx.conf file as I'm having some issues.
*Details*
I tried adopting the nginx.conf for CloudMan+CloudBioLiniux as described
Hello Lance,
I've committed a fix for this issue into the next-stable branch on the
galaxy-central repository in change set revision 9212:92c8a55a6679, so the fix
will be included in the upcoming Galaxy release. This fix is currently running
on both the test and main Galaxy tool sheds as
I am trying to upgrade cufflinks version from 1.3.0 to 2.0.2. I changed the
directory in the PATH to version 2.0.2 but when I run cuffdiff on the galaxy
it still uses the version 1.3.0. Do I need to change the code of the wrapper?
This is the right approach, but there must be a glitch
Hey y'all galaxiers,
Today, I tried to login using the testtoolshed web ui. To make sure that it
wasn't just isolated to an existing account, I created a new account, and still
I encountered the Server Error attached below. This error is not shown when
entering an invalid password. I was
Jorrit,
I may have been a bit unclear in my previous response. Allow me to
illustrate two scenarios:
First scenario:
1. A repository is created containing a BWA tool with version 0.5.9
2. The repository is installed to Galaxy.
3. New README file is uploaded, tool version is *not* changed.
Jorrit,
While I investigate the root cause of this, have you tried clearing all
cookies for testtoolshed.g2.bx.psu.edu?
--Dave B.
On 3/28/13 17:14:55.000, jorrit poelen wrote:
Hey y'all galaxiers,
Today, I tried to login using the testtoolshed web ui. To make sure that it
wasn't just
Hi all,
Is there a canonical list of current tool versions that are running in the
public galaxy? Is there a way to get that list? Also, I was hoping that
there might be a galaxy ami that I could use in the amazon cloud and by
that I mean NOT a cloudman instance. I am looking for an
Jorrit,
I've not been able to reproduce the first scenario using a local Galaxy
instance against the test tool shed. Could you tell me which revision of
Galaxy you're running when you encounter this behavior?
I do see that the revision bb20766df19c that you were initially trying
to update
Jorrit,
Thank you for the additional information, following those steps I was
able to reproduce the error and will be looking into the issue.
--Dave B.
On 3/28/13 18:04:48.000, jorrit poelen wrote:
Hey Dave,
I just reproduced this issue by:
1. clear all cookies (reset browser)
2. login
Hi all,
So I have a tool that I am writing a wrapper script for that produces a
directory of images as one of its outputs. This directory gets created
just fine in the job_working_directory, but then when the job finishes and
the contents of the job_working_directory are copied, the copy of the
26 matches
Mail list logo
