Aside: If I add steps to the beginning of the workfow, the step that
runs too early, typically occurs earlier in the flow. Can this indicate
a race condition where not all dependencies are available (stored?) yet
in the database at the time of querying for job eligible for queueing?
Best,
Gee
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
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 Bake
Hi all,
I am trying to get the *"tool_conf.xml"* 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: Picard(bet
Hi all,
I am trying to deploy Galaxy in my local server with some modifications.
But when I change the order of inside 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"* 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: Picard(bet
On May 20, 2013, at 3:08 PM, Nate Coraor wrote:
> On May 20, 2013, at 3:31 PM, Fields, Christopher J wrote:
>
>> On May 20, 2013, at 9:45 AM, Nate Coraor
>> wrote:
>>
>>> On May 19, 2013, at 11:41 PM, Fields, Christopher J wrote:
>>>
I've been seeing this error popping up quite a bit rec
On May 21, 2013, at 2:13 PM, Christopher Fields
wrote:
> On May 20, 2013, at 3:08 PM, Nate Coraor wrote:
>> ...
>> Hi Chris,
>>
>> We're disconnecting under all normal conditions and most error conditions -
>> it looks like only a few conditions would not properly disconnect:
>>
>> - If pbs_
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 inside
> in "tool_conf.xml" file , it's NOT taking effect. Should I
Hi all,
I am trying to deploy Galaxy in my local server with some modifications.
But when I change the order of inside 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,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 d
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, M
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,
>
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
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: 9320:47dd
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
th
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
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. 1
On Tue, May 21, 2013 at 7:36 AM, sridhar srinivasan
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 user or does not all
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
Hi Andreas,
try something like the following:
-l h_vmem=10G -pe "*" 20
Hope that helps,
Björn
> 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-
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 a
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 (b
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 tool_data_table_c
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 5/2
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 wrote:
> Hi Sridhar
>
> Since we are using MySQL for our Galaxy serv
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 co
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
On Mon, May 13, 2013 at 11:09 AM, Peter Cock 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
repositories reported as fai
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):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/2b35b5
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 liste
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
?user=galaxy&password
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
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=galaxy&password=password
it gave error in history page
"""
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