Aaanndd ofcourse it was due to the proxy settings.
I noticed that the history refresh is done through a call of the API and
since I had re-routed that to a different web server than the main server,
it broke.
But once I added this rewrite rule:
ReWriteRule ^(/api/histories/.*) http://lo
I do now actually get an error message in my browser saying "Error getting
history updates from the server. Internal Server Error"
Any ideas?
I suspect it is my proxy server settings but not sure.
Thon
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.p
Hhhmmm.. and now it doesn't and reproduces what Joachim reported...
-Oorspronkelijk bericht-
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex
Verzonden: donderdag 14 februari 2013 11:45
Aan: Greg Von Kuster; joachim.ja...@vib.be
C
There was a small, but important error in the proxy configuration...I had to pass the /api/ part to a proxy again with a [P] directive, not just the [L].So the correct proxy definition is: Options FollowSymLinks Order Allow,Deny Allow from all AuthType Basic AuthName "GALAXY@GHI. P
Hi, I am having a problem with running galaxy on the Amazon cloud. I have tried
this several times over the past few days, I followed the list and it seems my
instance is up and running. However, when I type the DNS in any browser it
can't connect to it. I am kind of aiming in the dark now becau
Hello Hakeem,
Here is a link to the tool shed wiki sections that provide all of the details
for installing repositories from the tool shed into your local Galaxy instance.
http://wiki.galaxyproject.org/Tool%20Shed#Installing.2C_maintaining_and_uninstalling_tool_shed_repositories_within_a_Galaxy_
HI,
Does anyone know who to install NGSRich software on a local instance of Galaxy?
I tried to install it from the shed_tool but it does not show up in the
repository, so I manually downloaded it from
http://toolshed.g2.bx.psu.edu/repository/view_repository?sort=name&operation=view_or_manage_rep
Hi,I have been struggling with setting up my galaxy system to allow it to use the LDAP authentication for users that come in through the frontend, while not wanting to have to use authentication when user want to access through the APII found some solution and I thought I'd share it with the wo
Hi,I have noticed that in the latest version of galaxy-dist, my history does not automatically update anymore.I have to press the refresh circle to have it update...I did change my proxy setup a little, so it would no longer require API calls to be authenticated, while access through the frontend w
On Thu, Feb 14, 2013 at 11:01 AM, Dannon Baker wrote:
> Could you share with me a file that reproduces this behavior? I'm
> unable to do so on a fresh -dist clone after trying various files and
> file types.
>
> Do you see any errors in the console or galaxy log when this happens?
>
I'm seeing t
This is a bug, and it's been fixed in this changeset:
https://bitbucket.org/galaxy/galaxy-central/commits/db08c095de0c249f3a6cde62f254c104de1fb6ea
Thanks for pointing it out,
J.
On Feb 13, 2013, at 8:25 PM, Anthonius deBoer wrote:
> Hi,
>
> One very cool feature was to be able to search
On Thu, Feb 14, 2013 at 10:30 AM, Nate Coraor wrote:
>
> You may be able to get this to work by setting 'display_servers =
> ' in your community_wsgi.ini file. This instructs
> Galaxy's remote user middleware to allow connections from this host even if a
> remote user has not been provided. I
Hi all,
I noticed that when I go in "Get Data" -> "Upload File from your
computer" (i.e. upload1 tool) the "File Format" list contains also
datatypes which have display_in_upload="false" in datatypes_conf.xml
(e.g. "afg", "fli"), while the list does not contain datatypes which
have no display_in_up
Hi all,
I've created Trello cards for both of these issues:
https://trello.com/card/jobs-stop-jobs-on-history-deletion/506338ce32ae458f6d15e4b3/626
https://trello.com/card/jobs-stop-job-function-in-jobs-admin-interface-is-broken/506338ce32ae458f6d15e4b3/627
--nate
On Feb 14, 2013, at 2:58 AM, H
Could you share with me a file that reproduces this behavior? I'm
unable to do so on a fresh -dist clone after trying various files and
file types.
Do you see any errors in the console or galaxy log when this happens?
On Thu, Feb 14, 2013 at 2:34 AM, Mathieu Bahin wrote:
> Hi,
>
> Thanks for t
Hi Nate,
I am sorry I missed your reply... Thanks for your input, will try this
soon.
Cheers,
Joachim
Joachim Jacob
Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib
On 02/13/2013 06:31 PM, Nate Coraor
Hi,
Thanks for the answer.
It is after the new galaxy-dist release and if a type is affected, all its
children types are too. For example the tabular but that's not the only one.
It's is not a question of size I think because very small datasets are not
displayed neither.
Cheers,
Mathieu
On Thu, Feb 14, 2013 at 10:40 AM, Nate Coraor wrote:
>> What I am facing, is that I have 100 FASTQ pairs or so, for a single
>> flowcell, I can start the analysis of that set from the UI, but it will just
>> crank through them and takes about 2-4 minutues for each pair to be
>> processed, so wi
On Feb 13, 2013, at 6:42 PM, Gaueko Erge wrote:
> Hi Nate,
>
> Thank you for your reply. After a lot of trying I was able to figure this out
>
> Entries in my alignsec.loc file were pointing to:
>
> seq AaegL1 /db/galaxydb/AaegL1/seq/
> seq AgamP3 /db/galaxydb/AgamP3/seq/
>
> and not
On Feb 13, 2013, at 5:56 PM, Anthonius deBoer wrote:
> Interesting!
> But maybe it is not the manager that is the bottleneck, but which process is
> the one that takes the inputs from the webpage (or in the API) and prepares
> all the files that are produced by the workflows?
>
> I guess it is
On Feb 13, 2013, at 3:25 PM, Carlos Borroto wrote:
> On Wed, Feb 13, 2013 at 3:10 PM, Greg Von Kuster wrote:
>> Carlos,
>>
>> Sorry you're having difficulty here. I'm not able to help very much here
>> because I'm not familiar with the Galaxy remote user authentication process
>> and I don't
Try using the Tophat test data to verify your installation; it's known to have
splice junctions:
http://tophat.cbcb.umd.edu/tutorial.html
http://tophat.cbcb.umd.edu/downloads/test_data.tar.gz
Good luck,
J.
On Feb 14, 2013, at 6:29 AM, Sachit Adhikari wrote:
> I tried with many data but still t
Hi Nate,
Thanks for your reply,
I guess the idea is that the job is prepared in the interface which lets
a user select
the grid. This is currently located in my galaxy instance as a if
statement in the
default job dispatcher. Just before it sends it to the job runner and
all the preparation
I tried with many data but still the same problem and regarding settings I
haven't changed a thing of Tophat2. What might be causing this error?
Thanks
On Wed, Feb 13, 2013 at 7:10 PM, Jeremy Goecks wrote:
> If the other outputs are fine, then the problem is likely with your data
> and/or your T
Hhhmm seems to behave normally in our running (latest) dist release
8530:a4113cc1cb5e tip
Alex
-Oorspronkelijk bericht-
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Greg Von Kuster
Verzonden: dinsdag 12 februari 2013 12:29
Aan: joachim.ja..
Hi Derrick,
We did that a year ago, while changing the mount point as
part of setting up a shared file system between our Galaxy
node and a cluster. Naturally we did a backup first, but I
don't recall any issues from this. At the time Nate just advised
not to have any jobs running at the time (and
Hi Nate,
copied datasets do work and I run Galaxy from the server root.
Thanks,
Sarah
- Original Message -
From: "Nate Coraor"
To: "Sarah Diehl"
Cc: "galaxy-dev@lists.bx.psu.edu List"
Sent: Wednesday, February 13, 2013 8:22:10 PM
Subject: Re: [galaxy-dev] Datasets linked into Galaxy
Just realized, you asked this question already. Please see:
http://dev.list.galaxyproject.org/Where-is-the-output-of-tools-stored-in-Galaxy-td4657655.html
where your question was answered by me and others on the list
Regards, Hans-Rudolf
On 02/14/2013 09:29 AM, Sachit Adhikari wrote:
I want
I want to redirect the output. For example the output of tophat2 is stored
in ./tophat2 I want to redirect it to my location.
On Thu, Feb 14, 2013 at 7:32 AM, Hans-Rudolf Hotz wrote:
>
> you can change the location where all the dataset files are stored in
> "universe_wsgi.ini":
>
>
> # Dataset
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