Hi Ambrose
simple answer: don't use Explorer and use Firefox or chrome instead.
I have tested the Nov. 4th release before updating our production server
and it worked on explorer 9 (on Windows 7). Nevertheless, I have been
running into the same issue during our Galaxy training course this
Hi Edgar
please find my comments within your text below:
On 12/11/2013 06:30 PM, fernandez Edgar wrote:
Hello,
My name is Edgar Fernandez. I’m a sys. admin. at University of Montreal.
I’ve been ask by a teacher to check out Galaxy.
So I’ve installed locally on my computer galaxy (I’m
Hi Sebastian
I am also not aware of any such documentation. It is probably impossible
to write it, as each such situation is different.
I don't quite understand what your 'script' is doing, but in your
situation, I recommend the following:
First of all, make sure you have a backup of your
Hi Thomas
Just double checking: what value are you using for the 'days' option?
If you use the default (which is 60 days if I remember correctly), only
data sets which have been 'deleted' more than 60 days ago will actually
be removed.
Regards, Hans-Rudolf
On 01/14/2014 09:49 AM, Thomas
Hi Christian
Have a look at the file: .hgignore
Regards, Hans-Rudolf
On 01/16/2014 03:23 AM, Cristian Alejandro Rojas wrote:
Hi all,
There is a setting on somewhere to skip the integrated_tool_panel.xml
file update?
Best regards,
--
*Cristian Alejandro Rojas Quintero*
/*Estudiante
Hi
I am sorry for hijacking someone else's thread:
3. teachers having read access to students’ work
This one is why I would give the teachers admin access - I think they
could impersonate the students to access their work (set
allow_user_impersonation = True in universe_wsgi.ini). It
Hi Ido
Over the last few years, we have moved our production server to
different hardware twice. And we also made copies of our production
server in order to have the right development environment.
It always work without much hassle, once we have taken care of the
'obvious', which usually
Hi Liisa
This rings a bell
I assume you use a MYSQL database? and I guess other pages are broken as
well?
We are also using MySQL and I had to fix several lines in several files
in order to get all report pages to work.
To do the fixes, have a look at this old (but still valid)
Hi Shenwiyn
Have a look at:
~/galaxy_dist/database/compiled_templates/base_panels.mako.py
Regards, Hans-Rudolf
On 02/17/2014 08:04 AM, shenw...@gmail.com wrote:
Galaxy developers:
I want to change my local Galaxy web layout,for example,delete the top
button of Visualization and Cloud or
Hi Alper
Have a look at ~/galaxy_dist/tool-data/shared/ucsc/ucsc_build_sites.txt
check the line starting with
main http://genome.ucsc.edu/cgi-bin/hgTracks?;
and add mm10
do a restart and you should get the link to 'UCSC main' for data mapped
to mm10
if that fixes the problem for
Hi Ravi
I don't quite understand question. It looks like you are mixing up two
different things? A few comments, which might clarify and help you:
- the postgresql db does not store the data. It tracks the users,
their jobs and their histories. Hence, it stays pretty small.
- the actual
Hi Milad
The error message: database is locked might be a hint.
Are you using a PostgreSQL database or just SQLite ? If the latter, you
will often run in troubles when running more than one job at a time, due
to file locking.
Regards, Hans-Rudolf
On 03/11/2014 07:41 PM, Milad Bastami
Hi Carrie
Was the history which is causing troubles created before you switched to
external authentication? Or has the user a slightly different e-mail
address now? eg different use of capital letters, like 'foo.bar@home'
and 'Foo.Bar@home' - we had such problems, when we switched to
Have a look at
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Switching_to_a_database_server
on how to set up the PostgreSQL database for Galaxy.
I am not aware of any tools to port the contents of the SQLite file to a
PostgreSQL database, except for setting up an
Hi Brian
It is difficult to imagine where such files are coming from. As each file in
~/database/files/*/ has a corresponding entry in the 'dataset' table. If you
have such files, then something went horribly wrong, eg by using two different
databases on the same files system. To double
Hi Lifeng
The easiest way to execute your script will be to provide a wrapper script
(written in your preferred language, eg Python, perl, etc). Call the wrapper
script like this:
commandwrapper $input $output1 $output2/command
and define $output1 $output2 according to your needs:
regardless of the original input-output format for standardized integration,
and possible automated integrations in the future.
On Tue, Mar 25, 2014 at 6:53 AM, Hans-Rudolf Hotz hansrudolf.h...@fmi.ch
wrote:
Hi Lifeng
The easiest way to execute your script will be to provide a wrapper
for the answer. But I'm afraid that detail panel does not
give me the path to the dataset. Have you encountered this problem before?
Nilaksha
On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi Nilaksha
Use the ! icon (View details) to get the full path
Hi Philip
The appearance of the visualization button depends on the datatype of
your output. E.g. when it is set to 'tabular', you should get the button
allowing you to create a scatter plot.
However, depending on your data, it might not make much sense to
visualize it in 'Trackster',
) column.
Hans-Rudolf
I wouldn't be surprised if something was wrong in my syntax. Thanks for
the help anyway.
Cheers,
Philip
2014-04-07 16:52 GMT+10:00 Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch:
Hi Philip
The appearance of the visualization button depends on the datatype
unwanted behavior in other context.
Anyway, all good, thanks for the help.
Regards,
Philip
2014-04-08 17:33 GMT+10:00 Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch:
On 04/08/2014 02:05 AM, Philippe Moncuquet wrote:
Hi Rudolph,
Thanks for the answer. I understand
Hi Nik
I don't think there is a solution out of the box for all of this, but I
will try to give you some pointers - others might have different or even
better suggestions (my suggestion are very 'hacky'). Let me answer your
questions in reverse order:
- Instead of using Add another file,
Hi Simon
I recommend the following (minimal) steps to migrate to a new server:
- set up the new server using the SAME Galaxy version your old server
is running.
- copy the contents of the 'database' directory
- make the site specific adjustment, e.g. universe_wsgi.ini
- connect your
example
of how one would create the file that the drill_down would use and then
how to use that file?
- Nik.
On Wed, Apr 9, 2014 at 1:13 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi Nik
I don't think there is a solution out of the box for all of this,
but I will try
Hi Brad
I don't you are using R to execute your R script
How do you call your R script, ie how does the command tag looks in the
tool definition file?
Also, why do you have a #!/bin/bash at the beginning of your R script?
Regards, Hans-Rudolf
On 04/27/2014 09:50 PM, Bradley Belfiore
$species $output
/command
So I believe Im calling R via the Rscript_wrapper.sh?
As far as the #!/bin/bash, not sure why I had that there, I took it out now.
thanks,
Bradley Belfiore
On Mon, Apr 28, 2014 at 9:25 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi Brad
I don't you
, there has been major changes introduced for the displays
with the release_2014.02.10 distribution. So, can anybody give me some
hints how to get this working again. I am happy to provide more details,
if required.
Thank you very much
Hans-Rudolf
--
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Trello cards
referenced in that e-mail for longer term fixes more appropriate for
public servers or servers where you don't or cannot trust your users.
-John
On Thu, May 8, 2014 at 7:39 AM, Hans-Rudolf Hotz h...@fmi.ch wrote:
Hi
This is long shot, but maybe someone can help us
We
Hi Nilaksha
I don't really understand your question, but a simple answer is:
Make a backup of the complete galaxy directory tree and make a backup of
your PostgreSQL database. You should do this anyway on a regularly
basis, if you use your Galaxy server in production. Since much more
likely,
Hi Ravi
To start, have a look at those wiki pages:
https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies
Regards, Hans-Rudolf
On 05/14/2014 06:43 PM, Ravi Alla wrote:
Hi All,
Due to the nature of our cluster we are not
Hi Neil
I am not aware of any (hidden) download options.
I usually go with 'copy-paste' and process in R or manually. Also, if I
need specific information which is often not displayed on the reports
page I get it directly out of the MySQL/PostgreSQL database. For such
cases it is handy to
Hi Emma
Have a look at
https://wiki.galaxyproject.org/Admin/Config/Access%20Control
and
https://wiki.galaxyproject.org/UserDefinedToolboxFilters
as an alternative you could also do a bad hack using dynamic_options
Regards, Hans-Rudolf
On 05/19/2014 10:38 AM, Emma Prudent wrote:
Hi,
I
On 05/26/2014 10:00 AM, Peter Cock wrote:
Hi Neil,
Via the GUI, if you are logged in as an administrator
(i.e. your email address is listed in universe_wsgi.ini)
there is a an admin tab (top banner, starting analyze
data etc). This includes an option to see the current jobs.
Via the command
Hi Shari
Have a look at the last few lines of the e-mail:
... To manage your subscriptions to this
and other Galaxy lists, please use the interface
at: http://lists.bx.psu.edu/
Hans-Rudolf
On 05/28/2014 03:56 AM, Shari Javadiyan wrote:
Hi all,
Is there any way to unsubscribes from
oops - forget to keep it on the list
Original Message
Subject: Re: [galaxy-dev] Move galaxy/database (SQLite) to a new location
Date: Wed, 04 Jun 2014 09:11:00 +0200
From: Hans-Rudolf Hotz h...@fmi.ch
To: neil.burd...@csiro.au
Hi Neil
First a little comment: I strongly
? There is no link from the database to
where the flat files are stored?
cheers
Neil
From: Hans-Rudolf Hotz [h...@fmi.ch]
Sent: Wednesday, June 04, 2014 5:11 PM
To: Burdett, Neil (CCI, Herston - RBWH)
Subject: Re: [galaxy-dev] Move galaxy/database (SQLite
Hi Wolfgang
short answer:
Please, put your package into the Galaxy Tool Shed. This makes it
visible to the whole Galaxy community and everybody can profit from it.
long answer:
I have been in the same boat. We never put the Galaxy wrappers and the
perl scripts of our old NGS pipeline
On 06/09/2014 07:33 PM, Malcolm Tobias wrote:
All,
I apologize for an off-topic question, by my update failed:
[galaxy@login002 galaxy-dist]$ /export/mercurial-1.7.5/bin/hg pull -u |
tee hg.pull.out
...
added 3716 changesets with 9929 changes to 2124 files (+46 heads)
...
merging
On 06/12/2014 12:06 AM, John Chilton wrote:
If anyone out there has tired using Galaxy with strictly MyISAM tables
and found it untenable - by all means please chime in.
Well, due to several reasons we are (still) using MySQL (version:
5.1.69) with only MyISAM tables. We have been
Hi Mark
There used to be a nice one: try adding '/mobile to your galaxy url.
It is still kind of working (just without the graphics), and it is
sufficient to monitor jobs.
Hans-Rudolf
There used to be one.
On 06/26/2014 08:03 AM, MF Rogers wrote:
I hope this isn't a FAQ; I have not yet
-Rudolf Hotz [h...@fmi.ch]
Sent: Thursday, July 17, 2014 5:42 PM
To: Burdett, Neil (DPS, Herston - RBWH); galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] cleanup_datasets.py not deleting files...
Hi Neil
The cleanup_datasets.py script only removes the files if older than the
time given (you did
Hi Julie
Are there any jobs running at all? What do you get when you click on
Manage jobs in the admin menu? Maybe you have some old jobs 'running'
which are now blocking your queue?
Hans-Rudolf
On 07/23/2014 11:14 AM, julie dubois wrote:
Hi all,
I've seen several posts for jobs which
+02:00 Hans-Rudolf Hotz h...@fmi.ch:
Hi Julie
Are there any jobs running at all? What do you get when you click on
Manage jobs in the admin menu? Maybe you have some old jobs 'running'
which are now blocking your queue?
Hans-Rudolf
On 07/23/2014 11:14 AM, julie dubois wrote:
Hi all,
I've
Hi David
There is another number, which might help you:
- there are over 1000 people on the dev-mailing list
(https://wiki.galaxyproject.org/GalaxyProject/Statistics#Membership)
assuming there are two galaxy admins per site - wishful thinking ;) -
and each site has on average two Galaxy
Hi Geert
A simple solution might be: you hand over a string containing all three
paths to your wrapper, and then the wrapper splits the string into the
three individual paths.
Hans-Rudolf
On 07/27/2014 04:44 PM, Geert Vandeweyer wrote:
Hi,
I'm working on tool wrapper that needs
?
This would require a custom .loc file
Hans-Rudolf
Geert
On 07/28/2014 09:33 AM, Hans-Rudolf Hotz wrote:
Hi Geert
A simple solution might be: you hand over a string containing all
three paths to your wrapper, and then the wrapper splits the string
into the three individual paths.
Hans-Rudolf
of that, and eventually, I will
do it. ;)
--
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
___
Please keep all replies on the list by using reply all
Of Hans-Rudolf Hotz
Sent: Tuesday, August 26, 2014 5:22 AM
To: galaxy-...@bx.psu.edu
Subject: [galaxy-dev] problems with database migration 119 - 120
Hi all
I am in the process of updating our galaxy servers (from release_2014.04.14 to
latest_2014.08.11).
when I execute
~/lib/galaxy/model
much for any hints and help
Hans-Rudolf
--
Hans-Rudolf Hotz, PhD
Bioinformatics Support
Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
___
Please keep all replies on the list by using
and the
Reference genome.
Hans-Rudolf
Thanks for the report and any info you can provide,
Carl
On Wed, Aug 27, 2014 at 4:03 AM, Hans-Rudolf Hotz h...@fmi.ch
mailto:h...@fmi.ch wrote:
Hi
As part of my upgrade/testing work, I am looking at the
visualization plugins.
In a new
Hi Carl
Thanks for your help - unfortunately no success so far
Let's try two things:
*First*, let's clear the browser cache to rule out that annoyance:
This didn't change anything. I have also tried different computers and
different browsers
*Second*, let's see what the server ends
Hi Robert
Are you using the built in SQLite database ?
Hans-Rudolf
On 08/31/2014 01:27 AM, Robert Baertsch wrote:
I submitted 13 fastq files to tophat2 using DRMAA and got this error.
Is it fatal? BTW: This is a super cool feature.
I’m running the following version of galaxy-dist.
Hi all
First of all, a big Thanks to Carl who helped me fixing this problem.
So as a summary for all, the problem was caused by a datatype (an
extension to tabular), I manually added to datatypes_conf.xml
Removing the datatype fixed the problem. I couldn't identify a syntax
problem, neither
On 09/12/2014 05:11 PM, Calvin Morrison wrote:
The stderr and stdout is empty, according to galaxy.
here is paster.log output for quikr when i run it.
galaxy.jobs.runners DEBUG 2014-09-12 10:33:45,997 (86) command is: # if
user == user quikr -v -k 0 -s
Hi Nikos
As a 'quick and dirty' work-around, I suggest generating in addition to
the output file a 'log' file, which can be read by the subsequent tool.
Hans-Rudolf
On 09/26/2014 04:54 PM, Peter Cock wrote:
On Fri, Sep 26, 2014 at 3:01 PM, Nikos Sidiropoulos
nikos.sid...@gmail.com wrote:
Hi Bongsoo
we had once a similar situation with one of our development Galaxy
installations. This was due to a change in the proxy settings of the server.
Regards, Hans-Rudolf
On 10/17/2014 01:06 AM, Bongsoo Park wrote:
Aysam,
Thanks for your reply. It works well on usegalaxy.org
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