It looks like the problem may have to do with the file I am using ???
It is a *.nii.gz file.
Does galaxy try to uncompress ? do something to *.gz files when using the api
(as it tries to do in ~/galaxy-dist/tools/data_source/upload.py
Does anyone know of where in the code I can edit so my mile
Hi,
Are there options available to track the actual runtime of jobs on a
cluster and store them in the database? Or are there fields in the
database that approximate the job execution duration?
This might be useful for fine-grained wall-time estimation in a crowded
cluster environment. What
On Wed, May 8, 2013 at 10:08 AM, Geert Vandeweyer
geert.vandewey...@ua.ac.be wrote:
Hi,
Are there options available to track the actual runtime of jobs on a cluster
and store them in the database?
Not yet, but I'd really like to have that information too.
Peter
On Tue, May 7, 2013 at 7:02 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Missing test components implies a tool config that does not define a
test (i.e, a missing test definition) or a tool config that defines a test,
but the test's input or output files are missing from the
On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
As you've already noticed, I've tracked down and fixed the main issue that
was causing inaccurate test results. Thank you again for the data you
provided, which was of great help narrowing down the cause of the issue.
Hi ,
I am getting error during Installing galaxy locally.
Traceback (most recent call last):
File
/illumina/apps/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py,
line 35, in app_factory
app = UniverseApplication( global_conf = global_conf, **kwargs )
File
Peter,
A technical issue prevented the tests from automatically running. I've
resolved the issue and started a manual run, you should be seeing test
results within 2-3 hours.
--Dave B.
On 5/8/13 07:09:28.000, Peter Cock wrote:
On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier d...@bx.psu.edu
Hi all,
Stupidly enough, I installed a tool shed repo under 'root' of the
toolbox. Yes, it was EMBOSS5.0 (btw, installation went flawless!).
1. From the admin menu, I choose to unactivate the repo (manage tool
shed repo's)
2. From the admin menu, I reinstalled the tool shed from Main Tool
Adam,
Normally, the Galaxy URL should be automatically determined and set in a
cookie during the repository installation process.
To help track down this issue, could you provide the revision of Galaxy
you're running, and the end of the paster.log file when this error occurs?
--Dave B.
Hi Sridhar
Have you set up your PostgreSQL database correctly? and provide the
right username and password in the 'universe_wsgi.ini' file ?
See:
In addition, it's helpful to know which browser you are using. Safari has
fairly strict policies on 3rd-party cookies if you have them blocked. Chrome
and firefox are less strict, so unblocking 3rd-party cookies if using Safari or
simply switching to chrome or firefox will probably solve this
+1 for me!
Alex
Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu]
namens Peter Cock [p.j.a.c...@googlemail.com]
Verzonden: woensdag 8 mei 2013 12:06
To: Geert Vandeweyer
Cc: galaxy-dev@lists.bx.psu.edu
Onderwerp: Re:
Joachim,
As you discovered, deactivating a repository does not give you the
option to select a new tool panel section. However, if you select the
option to remove the repository from disk, and then reinstall it, you
will be presented with the tool panel section page, where you can
uncheck
Hi Joachim,
can you try to delete/rename integrated_tool_panel.xml, it is generated
during start-up.
Hope that helps,
Björn
Hi all,
Stupidly enough, I installed a tool shed repo under 'root' of the
toolbox. Yes, it was EMBOSS5.0 (btw, installation went flawless!).
1. From the admin
Hi All,
I've been working to configure a new Galaxy instance to run jobs
under Condor. Things are 99% working at this point, but what seems to
be happening is after the Condor job finishes Galaxy tries to clean up a
cluster file that isn't there, namely the .ec (exit code) file.
Relevant
Hi Peter,
On May 8, 2013, at 6:45 AM, Peter Cock wrote:
On Tue, May 7, 2013 at 7:02 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Missing test components implies a tool config that does not define a
test (i.e, a missing test definition) or a tool config that defines a test,
but the
Hi All,
I've been working to configure a new Galaxy instance to run jobs
under Condor. Things are 99% working at this point, but what seems to
be happening is after the Condor job finishes Galaxy tries to clean up a
cluster file that isn't there, namely the .ec (exit code) file.
Relevant
Confirmed working, thanks!
-Branden
On 5/7/2013 1:25 PM, Dave Bouvier wrote:
Branden,
Thank you for reporting this issue, I've committed a fix in
9662:6c462a5a566d. You should be able to re-run your tool migration
after updating to that revision.
--Dave B.
On 5/7/13 11:09:31.000,
On May 8, 2013, at 10:08 AM, Branden Timm wrote:
Hi All,
I've been working to configure a new Galaxy instance to run jobs under
Condor. Things are 99% working at this point, but what seems to be happening
is after the Condor job finishes Galaxy tries to clean up a cluster file that
Hi all,
I'm fiddling with this, and I have a proof of principle working for PBS
jobs using very ugly sql-alchemy hack.
Idea is:
- if job goes from queued to running : store seconds since epoch in
'runtime'
- if job goes from running to finished : compare time, store difference
as runtime.
On Wed, May 8, 2013 at 3:28 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On May 8, 2013, at 6:45 AM, Peter Cock wrote:
On Tue, May 7, 2013 at 7:02 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Missing test components implies a tool config that does not define a
test (i.e, a
Nate, thanks for the tip. I'm adding some debugging info around that
block now to inspect what is going on.
One thing I just remembered (been awhile since I debugged Galaxy tools)
- does Galaxy still treat ANY stderr output as an indication of job
failure? There are two warnings in the
On May 8, 2013, at 12:21 PM, Branden Timm wrote:
Nate, thanks for the tip. I'm adding some debugging info around that block
now to inspect what is going on.
One thing I just remembered (been awhile since I debugged Galaxy tools) -
does Galaxy still treat ANY stderr output as an
Hi Sarah,
NCBI made some changes and the scripts to obtain all of this data in one
go are considered deprecated (for now - a ticket to update the scripts
is open here: https://trello.com/c/ehx5Gvr7). You may be able to work
out how to adjust them yourself, if familiar with how the data is
On Thu, May 3, 2012 at 12:20 AM, Cory Spencer cspen...@sprocket.org wrote:
Hi all -
I've been trying to get the repeat.../repeat tag working with a min
attribute for
some time now, though without any success. It works in other tools
distributed
with Galaxy, but when I attempt to use it
On Wed, May 8, 2013 at 5:40 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Cory,
Do you remember if you could solve this? I've used repeat a few times
even with a min value, but just hit the same issue as you:
AttributeError: 'ExpressionContext' object has no attribute 'keys'
...
On Tue, May 7, 2013 at 10:16 AM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Tue, Apr 30, 2013 at 2:04 PM, Dannon Baker dannon.ba...@gmail.com wrote:
Hey Dan,
Sure, you can configure per-tool job runners. This wiki page
(http://wiki.galaxyproject.org/Admin/Config/Jobs) should get you started,
Hello,
I've set up galaxy at the local linux. After data configuration, I run fastqc
to check how it runs. Here I got error message as below --
error
An error occurred running this job: Traceback (most recent call last): File
../galaxy-dist/tools/rgenetics/rgFastQC.py, line 158, in assert
Hello all,
The next
meetinghttp://wiki.galaxyproject.org/Community/GalaxyAdmins/Meetups/2013_05_15
of
the GalaxyAdmins
Grouphttp://wiki.galaxyproject.org/Community/GalaxyAdmins will
be held on May 15, 2013, at 10 AM Central US
I upgraded to the latest galaxy-central and got an error when running migration
script 115 which lengthens the password field from 40-255.
It failed saying that the table migration_tmp already exists. I ran this
without any existing database so I don't think it is anything on my end. Any
Hey Robert,
I assume this is sqlite? And, when you say you ran this without any
existing database -- was this was a completely new clone of galaxy, or did
you update a prior installation and delete database/universe.sqlite
manually before running?
-Dannon
On Wed, May 8, 2013 at 2:07 PM,
Hi Rudolf,
Thanks for the reply.
Previously i was using the
postgres://user:pass@host/galaxy in 'universe_wsgi.ini'
now i tried with
postgres:///db_name?user=user_namepassword=your_pass
and it is working.. but i could'nt connect to the webpage
http://127.0.0.1:8080/ from another system in
Hi,
I'm still struggling to get the example_watch_folder.py to work. So any
help much appreciated.
I've created a simple workflow, which essentially opens a text file and then
writes out the data to a html file.
My xml file:
tool id=CopyTool name=Copy Tool
descriptionTest/description
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