Hi,
When Galaxy is started the centre column displays the Hello world! It's
running ... WWFSMD? Html Page. How can this be changed so that a tool i.e. get
data tool is shown up on start-up with all its text boxes etc rather than the
default html file? Is this possible?
Thanks
Neil
Neil,
good news: the initial center panel renders static/welcome.html so easy to
change.
bad news: AFAIK no way to show a (dynamic) default tool form instead -
others may know more..
On Mon, Jul 29, 2013 at 5:03 PM, neil.burd...@csiro.au wrote:
Hi,
When Galaxy is started the centre
Hi,
A few days ago, I have installed the stable release of of Galaxy local
instance on my Workstation I am running it behind Apache web server proxy
.
In regard to the data snapshots, I've observed that, it is much more
organized on the Galaxy main rather than on my local instance.
For example,
Hi everybody,
In my lab, after upgrading our Galaxy instance to the latest version, we have a
problem with displaying tabular files.
Any idea from where the problem can come?
Thanks in advance to all.
Mish
Week 6 updates are here :
http://galaxy-gsoc2013.blogspot.in/2013/07/week-6-update.html
Thanks
Saket
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and other Galaxy
Thanks for the suggestin Linda...
i removed the line
-et NO_ET ##ET no phone home
Now i am not getting the Error as get key to run the GATK..
But i am getting error as the fasta file is not found..
even in backend i found the command as mentioned below
in the reference file section -R there
What is the problem you're observing, and do you see any errors in the
galaxy log or javascript console?
-Dannon
On Mon, Jul 29, 2013 at 5:51 AM, Misharl mon mish...@hotmail.com wrote:
Hi everybody,
In my lab, after upgrading our Galaxy instance to the latest version, we
have a problem
Dear all,
I'm running a local version of Galaxy using nginx as proxy and I have
problems with the visualization of remote tracks (like .bam or .bigwig)
on the UCSC genome browser. If I disable the anonymous login and then
try to display a .bam or .bigwig file on UCSC genome browser I get this
On Thu, May 2, 2013 at 4:29 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
For what is I think the second time (fortunately this was only on the
Test Tool Shed), I have managed to upload a tar-ball to the wrong
repository:
2:fae4084a0bc0
Hi Dave,
Did a Trello card get filled for this problem of failing tests on the Tool Shed?
Thanks,
Peter
On Tue, Jun 11, 2013 at 9:04 AM, Björn Grüning bjo...@gruenings.eu wrote:
Hi,
I also have that error in the latest toolshed:
AssertionError: Attempting to set field 'topology' to value
Hello all,
I'm seeing missing test results again on the Test Tool Shed, e.g.
listed under Latest revision: failing tool
testshttp://toolshed.g2.bx.psu.edu/repository/browse_my_writable_repositories_with_failing_tool_tests
I have:
http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
Tool
Hi Dannon,
Thank you very much for replying. The problem is that we cannot display any
tabular files in the galaxy result panel. The tabular files are correct. We
have checked the galaxy log, and didn't see anything.
Thank you,
Mish
Date: Mon, 29 Jul 2013 07:57:28 -0400
Subject: Re:
What happens when you attempt view the tabular file? Does it automatically
download instead of displaying, for example?
On Mon, Jul 29, 2013 at 9:54 AM, Misharl mon mish...@hotmail.com wrote:
Hi Dannon,
Thank you very much for replying. The problem is that we cannot display
any tabular
Peter,
I've created a Trello card where you can track this issue:
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
Most of these look like display issues, the test results are correctly
recorded in the database. I hope to have that and the seq_rename and
When i attempt viewing the tabular file, it doesn't download automatically. it
displays nothing, a blank panel.
Thanks Dannon
Date: Mon, 29 Jul 2013 09:55:10 -0400
Subject: Re: [galaxy-dev] Problem with tabular files
From: dannon.ba...@gmail.com
To: mish...@hotmail.com
CC:
I am referring to the following bug:
https://bitbucket.org/galaxy/cloudman/issue/6/tool-default-symbolic-links-to-mnt
We are waiting for this bug to resolve before we fix any other issues with our
Cloudman scripts. I am wondering when you think this bug will be resolved so I
can plan my time.
On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
I've created a Trello card where you can track this issue:
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
Thanks Dave.
Most of these look like display issues, the test results are correctly
We're working on it but don't have a specific ETA for the release of the
new volume. For now, you can continue to create and run non-migrated
clusters using the previous version of Cloudman using this launch form:
https://main.g2.bx.psu.edu/cloudlaunch?ami=ami-da58aab3bucket_default=gxy-workshop
On Mon, Jul 29, 2013 at 2:49 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Dave,
Did a Trello card get filled for this problem of failing tests on the Tool
Shed?
Thanks,
Peter
For anyone following this issue, on another thread Dave just replied:
Peter,
The issue with seq_rename
I'm finding it hard to deal with mutually exclusive options that also share
many options between them for certain command line tools. Functions of if
statements could solve this copy/pasting problem.
Thanks
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On Mon, Jul 29, 2013 at 5:35 PM, Ben Gift corn8b...@gmail.com wrote:
I'm finding it hard to deal with mutually exclusive options that also share
many options between them for certain command line tools. Functions of if
statements could solve this copy/pasting problem.
Thanks
Yes, it has if
Hi all,
Is there a target date for the next Galaxy release, or should that
differ, the next update to the main Tool Shed?
I'd like to start using reStructuredText README.rst files in my
tools which render much more nicely on the Test Tool Shed,
but are currently ignored on the Main Tool Shed
Peter,
From what I've been able to determine, the tmhmm_and_signalp test
results predate the introduction of the skip tool tests option, and the
script to check repositories for the presence of functional tests and
test data has been updating the last test date every day, hence the
On Jul 29, 2013, at 1:02 PM, Peter Cock wrote:
Hi all,
Is there a target date for the next Galaxy release, or should that
differ, the next update to the main Tool Shed?
Hi Peter,
The next release is planned for August 12. The next-stable freeze will occur
on 7/30 (tomorrow).
--nate
On Monday, July 29, 2013, Dave Bouvier wrote:
Peter,
From what I've been able to determine, the tmhmm_and_signalp test results
predate the introduction of the skip tool tests option, and the script to
check repositories for the presence of functional tests and test data has
been updating
Thanks Jeremy,
But this doesn't seem to work.
If I add the welcome_url to the universe_wsgi.ini (is this the universe config
file you mentioned?) as shown below, I continue to get the welcome.html page
# Galaxy
You'll need to add the setting further down in the config file, such as under
the 'UI Localization' section.
Best,
J.
On Jul 29, 2013, at 8:49 PM, neil.burd...@csiro.au wrote:
Thanks Jeremy,
But this doesn’t seem to work.
If I add the welcome_url to the
Yes I tried that but I still only see the default welcome.html page. Have you
got this to work?
Thanks
Neil
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Tuesday, 30 July 2013 12:37 PM
To: Burdett, Neil (ICT Centre, Herston - RBWH)
Cc: ross.laza...@gmail.com;
Hi
When starting Galaxy the tool panel and history panels appear as default.
On the bottom of these panels are two arrows to minimise / hide the panels. Can
someone show me how to make the panels be hidden by default rather than shown ?
Thanks
Neil
Hi,
I wish to import data into my local instance of galaxy from another website.
Kindly let me know how to achieve that and what all is required. I want to
import data from a chemoinformatic database (mainly compound structures) into
galaxy and run my own analysis tools on them.
Regards,
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