Hi Rudolf,
Thanks for the reply..
Could you please tell how to check and set the PostgreSQL ..
I provide the correct username and password in universe.ini file..
when i give
#database_connection = postgres:///galaxy_prod
?user=galaxypassword=password
it gave error in history page
Content
Dear list,
I recently updated our local Galaxy to galaxy-dist (version
9320:47ddf167c9f1, May 1st 2013). I noticed that the lock preventing new
jobs dispatching in Manage jobs of the admin panel is missing. Is this a
new feature? Or am I having problem with my configuration?
If this is indeed a
On 05/21/2013 11:22 AM, sridhar srinivasan wrote:
Hi Rudolf,
Thanks for the reply..
Could you please tell how to check and set the PostgreSQL ..
I provide the correct username and password in universe.ini file..
when i give
#database_connection = postgres:///galaxy_prod
Hi Greg Dave,
I'm trying to use the new inter-repository dependency mechanism
without explicitly naming the tool shed (i.e. assume the repository
is in the same ToolShed), as discussed here:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014736.html
My blast2go wrapper is currently
Hi Greg,
There may be an issue with the new feature to mark a specific revision
to skip tool tests. I ticked this earlier this week on this repository, yet the
tests appear to have been run overnight (and failed as expected):
On Mon, May 13, 2013 at 11:09 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
I remain puzzled why I am seeing seemingly stochastic missing test
results.
Hi Dave,
This continues - although I have been making progress with the
tests for some of my tools. Currently there are a number of
Hello Rudolf,
I tried with the IP address it gave the error as
Is the server running on host 192.168.1.1 and accepting
TCP/IP connections on port 5432?
Then i try with 0.0.0.0 again i got same error
OperationalError: (OperationalError) FATAL: Ident authentication failed
for user galaxy
Hi Sridhar
Since we are using MySQL for our Galaxy server, I am kind of running out
of ideas...and hope someone else on the list can spot the error in your
universe.ini file.
Just one last remark to double check:
Can you log into the PostgreSQL database with the same credentials from
the
Hello Rudolf,
Thanks for the reply..
I use the command you mentioned in reply..
and the error is psql: FATAL: Ident authentication failed for user
galaxy
Thanks
Sridhar
On Tue, May 21, 2013 at 4:53 PM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi Sridhar
Since we are using MySQL for our Galaxy
Peter,
The most likely cause of this is that there is an issue with some
preceding repositories that hang on installation, causing the build
process to time out and not test later repositories in the list. I am in
the process of working out a solution for that situation.
--Dave B.
On
Hello, Galaxy developers!
I do a bit of tweaking to a local galaxy instance. Thus, I just realized that
subdirectories are not supported for the location of .loc-files/data tables.
E.g. tool-data/somesub/my.loc is not recognized even if this location is correctly linked in
the
Geert,
This should be fixed in the up-to-date stable branch as far as I know. Can
you tell me what 'hg summary' states?
-Dannon
On Mon, May 20, 2013 at 4:43 PM, Geert Vandeweyer
geert.vandewey...@ua.ac.be wrote:
Hi,
After the latest upgrade (april), I'm having issues when starting
Hi,
I recently updated our local galaxy instance first time after a few month. Afterwards I noticed that
the way to setup job runners has changed from single lines to an extra XML-file.
I now started to write a job_conf.xml but I don't understand where I put the
parameters for GridEngine.
I
Hi Andreas,
try something like the following:
destination id=20cores_10G runner=drmaa
param id=nativeSpecification-l h_vmem=10G -pe * 20/param
/destination
Hope that helps,
Björn
Hi,
I recently updated our local galaxy instance first time after a few month.
Afterwards I noticed that
Thanks for your answer. I will try this.
But I must say I don't like this new style very much. I need to create an extra destination for
every paramater set. This blows up the configuration a lot.
regards, Andreas
On 21.05.2013 17:22, Björn Grüning wrote:
Hi Andreas,
try something like the
On Tue, May 21, 2013 at 7:36 AM, sridhar srinivasan
sridhar2bioi...@gmail.com wrote:
I use the command you mentioned in reply..
and the error is psql: FATAL: Ident authentication failed for user
galaxy
Your problem is then not in Galaxy. Your postgresql server either does
not have a galaxy
Hi,
I want to make workflows published on usegalaxy.org available for users on our local instance. How
do I do this?
regards, Andreas
--
Andreas Kuntzagk
SystemAdministrator
Berlin Institute for Medical Systems Biology at the
Max-Delbrueck-Center for Molecular Medicine
Robert-Roessle-Str.
hg summary:
parent: 9320:47ddf167c9f1 tip
Use Galaxy's ErrorMiddleware since Paste's doesn't return
start_response. Fixes downloading tarballs from the Tool Shed when
use_debug = false.
branch: stable
commit: 18 modified, 178 unknown
update: (current)
Geert
On 05/21/2013 04:59 PM, Dannon
This interaction is pretty clunky right now (I've made a trello card for
improving it: https://trello.com/c/eu8XiJLK.
Two options right now are:
1) Import (on main) each workflow you want to copy to your local instance,
and generate the regular download link for import. (Download or Export in
Ok, so you're running the old tip of -dist. There are a few new updates
you can retrieve using `hg pull -u -b stable
http://bitbucket.org/galaxy/galaxy-central`.
-Dannon
On Tue, May 21, 2013 at 12:01 PM, Geert Vandeweyer
geert.vandewey...@ua.ac.be wrote:
hg summary:
parent:
Hey Christian,
This is a bug that surfaced in revision 8333 which should be fixed
in 9326:d07c62f0067a, which is available in the most recent galaxy-dist
(stable branch). If you'd rather not update right away, we'll have another
full-fledged dist release out soon.
-Dannon
On Tue, May 21, 2013
Hey Joachim,
Thanks for pointing out the discrepancy here. I'll be overhauling the wiki
in the near future to correspond with a new Cloudman release and will make
sure to update this.
-Dannon
On Thu, May 16, 2013 at 10:01 AM, Joachim Jacob | VIB |
joachim.ja...@vib.be wrote:
Hi all,
I
Hey Rob,
Yes, you should be able to create your own volume and sub it into pd.yaml.
Since you want to share this across several instances, and you can't mount
an EBS volume to multiple instances, you'll definitely want to use the
snapshot method (and so, snap_id is required).
-Dannon
On Tue,
Hi,I am uploading a lot of data to our galaxy system, and it seems that the index creation is always happening on the server instance of the galaxy server and NOT on the cluster.This seems to be particularly true for BAM files, where the index creation is being done on the galaxy server and it is
Hi all,
I am trying to deploy Galaxy in my local server with some modifications.
But when I change the order of section inside toolbox in *tool_conf.xml
* file , it's NOT taking effect. Should I modify some other files to
change the order of display in the left pane??
Thanks,
VJ.
Hi VJ,
try to remove/remove integrated_tool_panel.xml and restart your galaxy
instance.
Cheers,
Bjoern
Hi all,
I am trying to deploy Galaxy in my local server with some
modifications. But when I change the order of section inside
toolbox in tool_conf.xml file , it's NOT taking effect.
On May 21, 2013, at 2:13 PM, Christopher Fields cjfie...@illinois.edu
wrote:
On May 20, 2013, at 3:08 PM, Nate Coraor n...@bx.psu.edu wrote:
...
Hi Chris,
We're disconnecting under all normal conditions and most error conditions -
it looks like only a few conditions would not properly
On May 20, 2013, at 3:08 PM, Nate Coraor n...@bx.psu.edu wrote:
On May 20, 2013, at 3:31 PM, Fields, Christopher J wrote:
On May 20, 2013, at 9:45 AM, Nate Coraor n...@bx.psu.edu
wrote:
On May 19, 2013, at 11:41 PM, Fields, Christopher J wrote:
I've been seeing this error popping up
Hi all,
I am trying to get the *tool_conf.xml* section code corresponding to
the following topics listed below. I am unable to find it in both the
default build and the stable build in bitbucket. If you can point me to
where I can find it, it'd be swell.
1) NGS: Variant detection
2) NGS:
Hi all,
I am trying to deploy Galaxy in my local server with some modifications.
But when I change the order of section inside toolbox in *tool_conf.xml
* file , it's NOT taking effect. Should I modify some other files to
change the order of display in the left pane??
Thanks,
VJ.
Hi all,
I am trying to get the *tool_conf.xml* section code corresponding to
the following topics listed below. I am unable to find it in both the
default build and the stable build in bitbucket. If you can point me to
where I can find it, it'd be swell.
1) NGS: Variant detection
2) NGS:
Hi Dannon,
I pulled the new updates and restarted galaxy. However, the issue is not
resolved. Is there other information you might need?
hg summary:
parent: 9332:0f51ae4f1c84 tip
Unicode fixes for workflow names in Tool Menu.
branch: stable
Best,
Geert
On 05/21/2013 06:08 PM, Dannon
Hi,I am trying to use the API to upload a file and since the upload can take a long time (see my previous post) I need to check if the upload has completed so I know I can start a workflow (or can I start a workflow even when the file is still in the "queued" state?)...I have successfully used the
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