Hi, Paul
I would like to know if mod_wsgi has been considered for the deployment of
Galaxy at all, and whether anyone has any positive or negative experiences
with it.
I can only speak for the second part of your question: I've had some
experience with Apache 2 + mod_wsgi, but within a Django
I'd also like to add in a way for the user to save/download the svg from
our visualizations that use it. Unfortunately, there's no
clean/straightforward way to do this. I've seen some solutions that are
better than nothing and it's on the list as well.
On Thu, Nov 15, 2012 at 2:45 PM, Jeremy
Hi Sascha and Ted,
The history panel is undergoing some major revisions and the omission of
the display icon was part of that. It will be re-added today.
Information from a jobs stdout and stderr are still be available using the
'i'nformation icon within each history item's display (You'll see a
Hi Sascha,
This may be due to the recent history panel changes. Can you update to the
latest revision and see if the error still occurs?
Thanks,
Carl
On Tue, Nov 20, 2012 at 2:22 AM, MSc. Sascha Kastens
s.kast...@gatc-biotech.com wrote:
Hi devs!
After updating my local instance to
AM, Carl Eberhard carlfeberh...@gmail.comwrote:
Hi Sascha and Ted,
The history panel is undergoing some major revisions and the omission of
the display icon was part of that. It will be re-added today.
Information from a jobs stdout and stderr are still be available using the
'i'nformation
Hi, Joachim
If you have access to your server logs, do you see any log messages
containing 'Error in history API' around the time those happen?
Is there a situation where this happens more often (or a way to reliably
reproduce)?
I'm unable to reproduce this locally so far.
The error definitely
The display icon has been re-enabled in revision 8634:b9d44cf4b68e.
Thanks for the catch/feedback.
On Wed, Jan 9, 2013 at 12:00 PM, Langhorst, Brad langho...@neb.com wrote:
In some cases (e.g. mira) it's nice to be able to follow what's going on
in the log file…
Does anybody else miss
Hello, Robert
When they mention the UCSC browser, is your user using the 'Get Data -
UCSC Main table browser' tool or are they trying the 'display at UCSC main'
link within a dataset in the history panel (which leads to the UCSC genome
browser display application)?
Does this problem still happen
, Peter Cock p.j.a.c...@googlemail.comwrote:
On Tue, Jan 22, 2013 at 4:43 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Short form:
Both the API and client side should handle single datasets error-ing
more
gracefully than they did and the history panel should be more
resilient and
useful
?
On Thu, Jan 24, 2013 at 6:12 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Wed, Jan 23, 2013 at 3:19 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Another thing you might try is to upload the file to our test server:
https://test.g2.bx.psu.edu/ and see if that works.
Thanks
, 2013 at 1:40 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
I was incorrect in stating that the changes in the next galaxy-dist will
help in this case, unfortunately. From the stack trace you posted, there
is
a deeper error with your instance that the client-side changes won't
help
Hello Anthonius,
Can you elaborate on how you're invoking the API? How are you calling it?
Thanks,
Carl
On Wed, Jan 30, 2013 at 6:30 PM, Anthonius deBoer thondeb...@me.com wrote:
Hi,
I am trying to use the API with my galaxy server running behind a proxy
server.
How do I pass
sys.exit(1)
.
.
.
/code
This will authenticate for each call and it seems to work nicely (if you
add the authenticate step to each of the functions, like I did here for
get
Thon
On Jan 31, 2013, at 11:44 AM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Hello Anthonius
Joachim, is your history panel still not updating or did you find a
solution from the info in this thread?
If not, can you post the contents of the alert/popup message?
Thanks,
Carl
On Tue, Jan 29, 2013 at 5:26 AM, Joachim Jacob |VIB|
joachim.ja...@vib.bewrote:
Hi,
I have a similar - but
the
full output, but, although the upload still fails, I don't get this
same traceback in the paster.log. I attach it anyway.
Thanks,
Dan
On Thu, Jan 31, 2013 at 12:15 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Ok - interesting!
Can you send me the paster.log from a daemon session
Just to be clear, Dan - this solved the login issue and not the upload
issue (in which case I'd owe Carlos a six-pack), correct?
C
On Mon, Feb 4, 2013 at 4:04 PM, Carl Eberhard carlfeberh...@gmail.comwrote:
Thanks much, Carlos - I owe you a beer!
On Mon, Feb 4, 2013 at 4:01 PM, Dan
Even better - thanks again, Carlos - and thanks for the help in tracking
this down, Dan.
On Mon, Feb 4, 2013 at 4:46 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Mon, Feb 4, 2013 at 1:21 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Just to be clear, Dan - this solved the login issue
Thanks much, Carlos - I owe you a beer!
On Mon, Feb 4, 2013 at 4:01 PM, Dan Tenenbaum dtene...@fhcrc.org wrote:
On Mon, Feb 4, 2013 at 11:45 AM, Carlos Borroto
carlos.borr...@gmail.com wrote:
On Mon, Feb 4, 2013 at 1:55 PM, Dan Tenenbaum dtene...@fhcrc.org
wrote:
Re: login: I believe
Hello, Roy
There was a recent fix for this. Is this problem still occurring for you?
Thanks,
Carl
On Thu, Jan 31, 2013 at 10:17 PM, Blum, Roy roy.b...@nyumc.org wrote:
Dear Galaxy support,
In the last 24 hours we are unable to load files to the Galaxy server.
We tried doing so as guest
we use on our main server. It may be a good
starting point.
Thanks,
Carl
On Thu, Feb 21, 2013 at 8:58 PM, shenwiyn shenw...@foxmail.com wrote:
**
Hi Carl Eberhard,
Thank you very much for you help.I have another some questions :
First,
we need to install the needed data,for example
concerned about now.I am so
thankful for some of you advice.
Thank you very much.
--
shenwiyn
*From:* Carl Eberhard carlfeberh...@gmail.com
*Date:* 2013-02-23 02:42
*To:* shenwiyn shenw...@foxmail.com
*CC:* galaxy-dev@lists.bx.psu.edu
*Subject:* Re
, Carl Eberhard carlfeberh...@gmail.com wrote:
Hello, Jason
At which revision of galaxy-central or galaxy-dist is your installation?
Does this happen intermittently or regularly (with every upload)?
Thanks,
Carl
On Mon, Feb 25, 2013 at 1:49 PM, Jason Evans jason.j.ev...@gmail.comwrote:
I
Hello,
We explored this for quite a while this afternoon and believe John is
correct about the location as well as the design decision.
It may be that the hashes generated in some instances will correctly parse
as 16 digit integers and, since an integer lookup is tried first (and you
may either
Hello,
Does applying the patch from [galaxy-dev] Strange issue where the dataset
reported in the bug report doesn't correspond to the current dataset help?
If not, we can diagnose further. Thanks,
Carl
On Fri, Mar 8, 2013 at 3:35 PM, Jean-Francois Payotte
jean-francois.payo...@dnalandmarks.ca
Hello, all
Thanks to you both for reporting this.
John, in the steps to reproduce you mention, is step 4 going through the
browser?
If using curl/wget with an api key, they should of course, allow you to
retrieve all histories (logged in or not).
If through the browser, where you able to
!
*Jean-Francois*
From:Carl Eberhard carlfeberh...@gmail.com
To:John Chilton chil...@msi.umn.edu
Cc:Jean-Francois Payotte jean-francois.payo...@dnalandmarks.ca,
galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Date:08/03/2013 06:07 PM
Subject
clicking the bug button. If I encounter any
issue I will post back.
-Eric
-Carl Eberhard carlfeberh...@gmail.com wrote: -
To: Eric Enns eric.e...@phac-aspc.gc.ca
From: Carl Eberhard carlfeberh...@gmail.com
Date: 03/12/2013 10:15AM
Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu
Hello, Stephanie and Julien
What revision are you using IGBMC?
Can you clarify what you mean by a private dataset? Are non-owners
importing into a history via a shared history, or are they being passed a
direct link to the UCSC display viewer from the owner?
Thanks for the information,
Carl
Hello, Julien
Please see my reply and questions to Stephanie in her latest update.
Thanks,
Carl
On Mon, Mar 18, 2013 at 2:20 PM, Julien SEILER seil...@igbmc.fr wrote:
Hi all,
We have installed a local galaxy server and we are encountering a problem
when trying to use UCSC display
Hello, Shaun
Which revision of galaxy-central or galaxy-dist are you using in your local
install?
Thanks,
Carl
On Wed, Mar 20, 2013 at 12:52 PM, Shaun Webb swe...@staffmail.ed.ac.ukwrote:
Hi Jen, I should have said this is in my own install. It works fine at the
main server.
I only
Hello, Greg,
If I understand correctly, this may be an error with the server or panel
loading the previously-used/most-current history. How many histories are
displayed when you use the 'history-options-button' (the gear at the top of
the history panel) and click 'Saved Histories'?
As a side
Thanks much for the information, Geert. I've created a card for this bug in
Trello: https://trello.com/c/KLmH1nag.
On Wed, Apr 3, 2013 at 5:39 AM, Geert Vandeweyer geert.vandewey...@ua.ac.be
wrote:
Hi,
In case anybody is wondering, the set_user_disk_usage.py script corrects
this.
Best,
Hello, Hakeem
Although I've never used it, you might try the java_genomics_toolkit
available as a tool shed repository (or have your installation's admin
install it). It contains a tool called 'Align values in a matrix' which may
work for your needs.
Thanks,
Carl
On Tue, Apr 2, 2013 at 12:51
Hello, Sridhar.
Can you tell me the browser and operating system you're using?
Thanks,
Carl
On Mon, May 13, 2013 at 6:50 AM, sridhar srinivasan
sridhar2bioi...@gmail.com wrote:
Hi after installing galaxy,
i could'nt see the history page in right end of galaxy web.
it shows
Content
it's set to?
Carl
On Tue, May 14, 2013 at 12:01 AM, sridhar srinivasan
sridhar2bioi...@gmail.com wrote:
Hi Carl,
I am using firefox 3.6.18 and linux Red Hat/3.6-1.el5_6..
Thanks
Sridhar
On Mon, May 13, 2013 at 8:31 PM, Carl Eberhard carlfeberh...@gmail.comwrote:
Hello, Sridhar.
Can
Hello, מירב
It looks like the indexing system/format in 'bwa index' has changed
and we haven't updated the wiki to reflect the changes.
The reverse index (which includes the .r* files) are now part of the
forward index. You
should be fine to proceed.
I'll update the wiki to reflect this.
From
Hello, Shashi
It looks like TreeViewX was written in C++ as a desktop program. In this
case, there is no way that it can be used with the display_application code
without major modification.
One option is to not use TreeViewX from within Galaxy but simply have it
installed on your users'
Hi, Ambrose
A couple of places to start:
Did the javascript console (in Firefox: Tools-Web Developer-Web
Console) display any errors when you reloaded the failing saved history
page?
What does is the output of 'hg summary' when run in a terminal from your
Galaxy root directory?
I believe
Hello, Sridhar
How large is the file you're trying to plot?
The scatterplot visualization doesn't do well with large datasets (more
than ~10,000 points). I'm working to provide some form of pagination, but
it may take some time.
If your file is large, filtering or splitting up your data may
Hello, Phillip
I haven't been able to replicate this yet (https://trello.com/c/LdLlJDo9).
Do you see any errors in your log near or after GET /history/list
HTTP/1.1?
Shane Sturrock worked around this problem by updating his universe_wsgi.ini
file (if I understand his procedure):
1. Make a backup
-317-485786
F: +31-317-483342
E-mail: philip.degr...@wur.nlmailto:philip.degr...@wur.nl
Internet: http://www.nutrigenomicsconsortium.nl
http://humannutrition.wur.nl/
https://madmax.bioinformatics.nl/
From: Carl Eberhard [carlfeberh
for the reports and the help in tracking it down.
Carl
On Tue, Jul 16, 2013 at 4:06 PM, Carl Eberhard carlfeberh...@gmail.comwrote:
Nice catch!
I'll see where this leads.
On Tue, Jul 16, 2013 at 7:03 AM, Groot, Philip de
philip.degr...@wur.nlwrote:
Hi Carl,
Thank you for your quite
That's both a bug (should default to 'unspecified') and a usability issue
(sorting the genomes). I've added a card:
https://trello.com/c/Hr1JdeGq/1007-ui-bug-genome-selection-when-adding-library-data-files
On Thu, Jul 11, 2013 at 11:06 AM, Lionel Guy guy.lio...@gmail.com wrote:
Hi Galaxy-devs,
Hello Mark,
Can you post the output entry from your tool xml for that file?
Thanks,
Carl
On Mon, Jul 15, 2013 at 5:15 PM, mark.r...@syngenta.com wrote:
Hi All
** **
I’m trying to format one of the three outputs of my galaxy tool as plain
text. Thus far no matter how I specify my
Hey, Seth
I'm using npm less 1.3.3. That error isn't a known issue, no.
Is that the full stack trace/error report? Which files have you edited?
Thanks,
Carl
On Tue, Jul 30, 2013 at 2:39 PM, Seth Sims seth.s...@gmail.com wrote:
Dear Galaxy devs,
I am attempting to create a style
/nodejs/less/index.js:113:15
make[1]: *** [base.css] Error 2
make[1]: Leaving directory `/srv/galaxy-dist/static/style/blue'
make: *** [all] Error 2
Which is apparently a bug in the version of lessc I have.
On Mon, Aug 5, 2013 at 11:09 AM, Carl Eberhard carlfeberh...@gmail.comwrote:
Hey
, 2013 at 11:56 AM, Carl Eberhard
carlfeberh...@gmail.comwrote:
The ini file is not a .less file so it will error if you call lessc
directly with it.
It may be that you're lacking some (not obvious) dependencies. Do you
have pyparsing and PIL installed and available in your terminal (pip
That's a great point. I've made a bug card for it here:
https://trello.com/c/LsZoPtwv/1053-jobs-better-unicode-handling-in-stderr
Thanks for reporting this.
Carl
On Sat, Jul 6, 2013 at 11:33 PM, Kyle Ellrott kellr...@soe.ucsc.edu wrote:
This also took out my job handlers (exception below). So
Hello, Cristopher
Thanks for noticing this. I've updated the wiki entry:
http://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files#Number_of_Output_datasets_cannot_be_determined_until_tool_run
Does the line starting with 'Alternately,' match the behavior you're seeing?
Thanks,
Carl
)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/
On Tuesday, September 3, 2013 at 12:45 PM, Carl Eberhard wrote:
It is web-specific and only handles the mako/static serving cases. I
think the only areas we were generalizing
/2d0bcb07596c4c688ed3908391d866831c65c042/lib/galaxy/web/base/pluginframework.py?at=default
It should at least be easier modify. Have a look and let me know if you see
any issues or have suggestions.
On Tue, Sep 17, 2013 at 11:19 AM, Carl Eberhard carlfeberh...@gmail.comwrote:
Heya, Michael
Heya, Andy
Galaxy hasn't been designed to be loaded in an iframe yet.
Currently, the javascript in Galaxy makes use of the window variable top -
which points to the highest browser window in the DOM. There are many
instances where we rely on both 'top' and the link target '_top' to control
the
Hi, Nikolai
This should have been fixed with commit 10200:fd4113962c32 to the stable
branch. What version are you using?
Thanks
On Wed, Oct 16, 2013 at 8:19 AM, Nikolai Vazov n.a.va...@usit.uio.nowrote:
Hi,
I have discovered the following weird Galaxy behaviour. If one sets
log_actions
code is not in central however it might be related to recent
changes to the history panel. Carl Eberhard might now more, adding him to
the conversation.
--Marten
On Mon, Nov 4, 2013 at 2:45 PM, Robert Baertsch baert...@soe.ucsc.eduwrote:
It keeps doing posts, and I'm not seeing any new
Hello, Peter.
Thanks for the report. There was an error in the javascript error handling
of purge_async which is now fixed in stable:11227:151b7d3b2f1b.
In the instances you mention, you should now see an error message in the
history 'Unable to purge this dataset': This is because of two
Hello, Stephen
Although still under initial development, you may want to look into the
visualization registry for the infrastructure to render the region and
allow the user to interact with it:
http://wiki.galaxyproject.org/VisualizationsRegistry
Hello, Karen
This is a bug and I wanted to let you know I'm looking into it now:
https://trello.com/c/dzBmbyqF
Sorry for the frustration and thanks for the report,
Carl
On Mon, Dec 2, 2013 at 6:23 PM, Karen Miga khm...@soe.ucsc.edu wrote:
Hello,
I am trying to use phyloviz on the
know if I can help further.
On Thu, Dec 5, 2013 at 3:08 PM, Carl Eberhard carlfeberh...@gmail.comwrote:
Hello, Karen
This is a bug and I wanted to let you know I'm looking into it now:
https://trello.com/c/dzBmbyqF
Sorry for the frustration and thanks for the report,
Carl
On Mon, Dec 2
Hello, Edgar - thanks for installing Galaxy!
Regarding the screenshots: it looks like Galaxy's static css stylesheet
isn't being loaded properly. Is this still occurring for you? Do you see
anything when you try to go to http://localhost:8080/static/style/base.css
in your browser? (You should see
Hi, Federico
Starting with the next distribution (and in the current 'galaxy-central'),
you'll be able to do just that.
Here's the documentation for it:
https://wiki.galaxyproject.org/Learn/Managing%20Datasets#Searching_Datasets
In future releases, we hope to enable the use of multiple
Hey, Bjoern
Not sure whether a pull request or a toolshed repo would be best, but: if
you decide on a toolshed repo, graphview as it is should be able to use
your datatypes if they include a 'node-edge' dataprovider.
Also, graphview is on my list - but most likely I won't get to it in the
near
Hi, Carrie
Can you (or the other user) open the javascript console and try to load the
history again in order to reproduce the problem?
You can open the console:
- by going to the menu command: Tools-Web Developer-Web Console in
Firefox.
- going to: the 'control menu' (the three horizontal bar
Graduate Student Association, University of Georgia
mepcotter...@gmail.com (mailto:mepcotter...@gmail.com)
mepc...@uga.edu (mailto:mepc...@uga.edu)
m...@cs.uga.edu (mailto:m...@cs.uga.edu)
http://michaelcotterell.com/
On Wednesday, September 18, 2013 at 11:00 AM, Carl Eberhard wrote:
I've
Thanks, Ravi Peter
I've added a card to get the allow_user_dataset_purge options into the
client and to better show the viable options to the user:
https://trello.com/c/RCPZ9zMF
On Fri, Mar 14, 2014 at 11:10 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Fri, Mar 14, 2014 at 11:24 AM,
if I can find out the answer to your question on the cleanup
scripts.
On Tue, Mar 18, 2014 at 10:49 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Tue, Mar 18, 2014 at 2:14 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Thanks, Ravi Peter
I've added a card to get
this dataset' link in deleted datasets.
I'll see if I can find out the answer to your question on the cleanup
scripts.
On Tue, Mar 18, 2014 at 10:49 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Tue, Mar 18, 2014 at 2:14 PM, Carl Eberhard carlfeberh...@gmail.com
wrote:
Thanks, Ravi Peter
Hello,
That's a good question! Does the size in the top right change when the page
is reloaded? Are these datasets copied from another history?
How are you purging the datasets? As Dannon mentioned, if you click the 'X'
button on the dataset it will 'mark' the dataset as deleted. To permanently
deleted and removed
from disk. But I am not sure if there is any difference with the 3-steps
that you advised. I think the difference might be that it can purge the
dataset one by one in your advice, is it?
Thanks
Xiaofei
*From:* Carl Eberhard [carlfeberh...@gmail.com]
*Sent:* Monday
)
Hope that helps. We’re very new to Galaxy so I won’t be surprised if it’s
something wrong on my end.
Thanks,
Dori
*From:* Carl Eberhard [mailto:carlfeberh...@gmail.com]
*Sent:* Monday, July 28, 2014 10:55 AM
*To:* Björn Grüning
*Cc:* galaxy-dev@lists.bx.psu.edu; Sajdak, Doris
Hi, Hans,
What was the datatype (listed as 'format') of the dataset you tested with
here?:
However, if I hoover over the bar-plot icon, Visualize in Trackster pops
up (instead of just Visualize)
Trackster by default accepts all datatypes (all subclasses inheriting
data.Data) and is the only
(oops, to continue the truncated sentence in the prev. email):
You can change that by editing the ...
config/trackster.xml 'datatype' as you did in your email to restrict what
Trackster can run on.
(sorry about that)
On Wed, Aug 27, 2014 at 9:39 AM, Carl Eberhard carlfeberh...@gmail.com
wrote
Ok - thanks! That is strange: the server seems to be configured properly
for all the new plugins but the client side believes only trackster is
available.
Let's try two things:
*First*, let's clear the browser cache to rule out that annoyance:
- In Chrome, I've had good luck with these
Ok. Very strange. I'm unable to reproduce this with galaxy-dist 57d1b77
(stable).
Can you apply the attached patch, load a history with a simple bed file
(say: test-data/1.bed - or any bed file), and reply with what the logs say?
You can safely revert that change after we're done.
On Thu, Aug
Hi, Saket
There's currently no json dataprovider.
It's still relatively easy to get a JSON object, though. I'd recommend:
1. Using the 'line' dataprovider
2. Then, joining the strings returned from it (generally, you want all
the strings so be careful using the regex, limit, or offset
74 matches
Mail list logo
