Hello everyone,
We are considering to deprecate the Sample Tracking feature in Galaxy
18.01. Please let us know if you are using it so we can discuss alternative
options.
Thanks,
Sam
___
Please keep all replies on the list by using "reply al
thing, I was hoping
> that it works out of the box :).
>
> Could you point me to some documentation where the setup is explained?
>
> Best,
> Matthias
>
> On 25.08.2017 19:05, Aysam Guerler wrote:
>
>> Hi Matthias,
>>
>> Have you added the visulization t
Hi Matthias,
Have you added the visulization to Charts or the regular Galaxy
visualization framework? If it is the latter please make sure that you
correctly specified the datatype in your XML file. Your visualization
should than appear in the drop-down list in the history.
Thanks,
Sam
On Fri, A
Thanks for reporting this. A PR which should fix this issue is available
here:
https://github.com/galaxyproject/galaxy/pull/4496
On Fri, Aug 25, 2017 at 7:43 AM, SAPET, Frederic <
frederic.sa...@biogemma.com> wrote:
> Hi
>
> Same behavior for me.
> Chrome (60.0) and IE (11.0.9600) are fine.
>
> F
Fyi. This has been resolved. The issue was related to server rewrite
settings. A remaining question is if external users are able to change
individual user settings.
On Mon, Aug 21, 2017 at 7:31 PM, evan clark wrote:
> I have been testing our new galaxy instance and came across an odd issue.
> W
Thanks for reporting this. Have you tried to refresh the browser?
On Mon, Aug 21, 2017 at 7:31 PM, evan clark wrote:
> I have been testing our new galaxy instance and came across an odd issue.
> When a user is logged in and attempts to set their preferences the view
> does not render and the gal
Sorry for the late response. So the venn diagram visualizes the overlap
between sets. Each set is represented by entries in a column e.g.
#SET1 SET2 SET3
A GA
B HB
C AG
D BH
E CX
F DZ
I hope this helps
I agree, it should be straightforward. I will look into it.
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Hey,
There is no documentation for this but it is possible. You need to install
R and two R libraries (getopt, Matrix) in order to execute the charts
R-script. Once R is configured you can add the charts tool to the tools
directory and update your config/tool_conf.xml file accordingly before
resta
Hi Fabien,
Are you referring to the entries shown in the drop-down when you click on
the select field? Can you send a screenshot?
Thank you,
Sam
On Thu, Jul 13, 2017 at 5:50 AM, fabien gogé wrote:
> Dear All,
>
> I try to column options for a param linked to a dataset contained in my
> history
Hey,
We are trying to resolve the issue so that others do not have to change the
Apache settings.
Is it possible to test this potential fix here:
https://github.com/galaxyproject/galaxy/pull/4225 and comment on the issue?
Thanks in advance,
Sam
On Thu, Jun 15, 2017 at 5:13 PM, Nicola Soranzo w
Hi Matthias,
Can you verify that the file is recognized as 'sif'-file in the Galaxy
history and not as 'txt'-file? Please change the format if necessary.
I hope this helps,
Sam
On Wed, Apr 5, 2017 at 7:01 AM, Matthias Bernt wrote:
> Dear galaxy-dev,
>
> I just wanted to test the exciting cytos
want to add our
>> tools and the datatypes to galaxy. I'm not sure how to get around to doing
>> it without rpy2. I'd like to keep a sniffer function in there.
>>
>> Thanks again,
>> Cris
>>
>> On Tue, Dec 13, 2016 at 1:24 PM, Aysam Guerler
&g
Hey Cris,
Dannon and I figured out, that the problem is that your datatypes are not
loaded properly, due to these two invalid imports:
https://github.com/ImmPortDB/immport-galaxy/blob/release_16.07/lib/galaxy/datatypes/flow.py#L13
Removing them fixes the issue. The error for this is shown in the
Ok, let me look a little bit further then. Can you send me the
corresponding tool xml file and let me know which datatypes appear in the
dropdown list and which of those you would not expect to see? Ideally we
can reproduce it with datatypes available to everyone, so I can test it
locally.
Ok, so this seems to work properly, and implicit conversion is the reason
why you see html and text, but not png and pdf files. Currently there is no
option to disable implicit conversion but its an enhancement we can suggest
to be implemented by creating a github issue.
___
accepting several datatypes.
> thanks for your help!
> -Cris
>
> On Mon, Dec 5, 2016 at 10:29 AM, Aysam Guerler
> wrote:
>
>> Hey Cris,
>>
>> Thanks for reporting this. I am looking into it. In the meanwhile, I am
>> wondering if you can reproduce the erro
Hey Cris,
Thanks for reporting this. I am looking into it. In the meanwhile, I am
wondering if you can reproduce the error on usegalaxy.org? Does it happen
for all tools?
Thanks,
Sam
On Mon, Dec 5, 2016 at 8:47 AM, Cristel Thomas
wrote:
> Hi Galaxy Devs,
>
> We have a few tools with multiple d
Hey Katherine,
It happens in basic.py. The code tag is executed to generate select options
there. Look at:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/parameters/basic.py#L778
Bye, Sam
On Mon, Nov 21, 2016 at 1:46 PM, Peter Cock
wrote:
> Are you asking how Galaxy takes th
rded message --
> From: Katherine Beaulieu
> Date: Mon, Oct 24, 2016 at 2:55 PM
> Subject: Re: [galaxy-dev] Workflow Execution Files
> To: Aysam Guerler
>
>
> Awesome thanks Aysam! I was wondering if you know what happens to the job
> parameters once they go throu
Hi Katherine,
The tool form is build and submitted to the API through
tool-form-composite.js.
Sam
On Mon, Oct 24, 2016 at 9:29 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Hi Everyone,
> Does anyone know what files workflow execution goes through? I had assumed
> it just w
I remember this issue and that it was fixed. Updating to a newer revision
should resolve it.
On Wed, Jul 27, 2016 at 10:06 PM, Dannon Baker
wrote:
> This is indeed weird behavior. What revision is your Galaxy at?
>
> On Wed, Jul 27, 2016 at 9:07 PM Cristel Thomas
> wrote:
>
>> Hi all,
>> I ran
Hi Mohamed, the masthead file has been moved to
https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/layout/masthead.js
.
On Tue, May 17, 2016 at 4:12 AM, Mohamed Kassam wrote:
> Dear all,
> I would like to know which file replaced the galaxy.masthead.js file.
> Because I was p
Thanks Peter. I think you are right and that its a change in Galaxy which
causes this routing issue. I have prepared a fix for it:
https://github.com/galaxyproject/galaxy/compare/dev...guerler:fix_upload_link_000?expand=1.
Ill double check tomorrow with those working on the routing and then issue
a
No worries. Although it is 'deprecated' it will be not be removed until we
have a good alternative.
On Wed, Jan 27, 2016 at 4:36 AM, Matthias De Smet
wrote:
> So it seems it has been deprecated a bit prematurely. Maybe the Galaxy
> team should “undeprecate” it untill a viable alternative is foun
Thx for reporting this. I am looking into it.
On Wed, Nov 25, 2015 at 4:53 AM, Nils Paulhe wrote:
> Hi!
>
> Same problem here but only if my workflow start with an "input type" tool
> or any other tool, i can not select an option in list for workflow's other
> tools
> cf:
> https://dl.dropboxuse
Well I guess it doesn't matter, glad it works now.
On Wed, Sep 30, 2015 at 2:47 PM, Aysam Guerler
wrote:
> If the select field did not properly render before, it should not render
> properly now.
>
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If the select field did not properly render before, it should not render
properly now.
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Galaxy root. Is this still the
> advised approach, or should the tool that requries test_select_options.txt
> be of type “manage_data”?
>
> Thanks!
>
> Greg
>
>
> On Sep 18, 2015, at 9:42 AM, Aysam Guerler
> wrote:
>
> Hi Greg,
>
> The tool form supports multiple dynam
Hi Greg,
The tool form supports multiple dynamic fields which depend on each other.
You may want to take a look at this:
https://trello.com/c/NOmjJxCi/428-305-potential-bug-in-dynamic-options-filters
.
Hope this helps,
Sam
On Fri, Sep 18, 2015 at 8:30 AM, Greg Von Kuster wrote:
> Hello all,
>
Hey Linda,
This seems to be an issue which has already been fixed. Could you please
update your instance and/or let me know at which commit it is?
Thank you,
Aysam
On Thu, Apr 30, 2015 at 6:41 AM, Linda Bakker wrote:
> Hi All,
>
> I am relatively new to galaxy and recently had to take over the
Hi Damion,
An initial implementation of the library dataset tool parameter (which
allows the selection of multiple library datasets) is currently in the
pipeline https://github.com/galaxyproject/galaxy/pull/132. After some
review the feature should be available in the default branch, however you
m
A fix for this is on the way.
On Fri, Mar 27, 2015 at 10:53 AM, Peter Cock
wrote:
> Hi all,
>
> Unfortunately it appears that the new-look check box controls are wrongly
> defaulting to ticking the first item rather than following the defaults
> given.
>
> This is a recent regression which I not
Hi Michael,
We have update the repository. Please re-install the Charts plugin. It
should work now.
Thanks,
Sam
On Tue, Feb 24, 2015 at 9:39 AM, Michael Thon wrote:
> Hi -
> I tried to install the package charts but it failed on the dependency
> charts_r_packages with this error:
>
> File
> "/
Hey Damion,
Thanks a lot for the description. We are currently switching the tool form
to a newer version but I will look into this fix soon and should be able
transfer it.
Thanks,
Sam
On Tue, Jan 20, 2015 at 2:45 PM, Dooley, Damion
wrote:
> I was successful getting library dataset selection a
Hi Damion,
This change here
https://bitbucket.org/galaxy/galaxy-central/pull-request/639/fix-for-librarydatasettoolparameter/diff
might fix it.
Thanks for reporting the issue,
Sam
On Thu, Jan 15, 2015 at 3:42 PM, Aysam Guerler
wrote:
> Hi Damion,
>
> I will look into this.
>
>
Hi Damion,
I will look into this.
Thanks,
Sam
On Thu, Jan 15, 2015 at 3:30 PM, Dooley, Damion
wrote:
> Hi,
>
> Almost!
>
> def get_initial_value( self, trans, context, history=None ):
>
> in /lib/galaxy/tools/parameters/basic.py under class
> LibraryDatasetToolParameter( ToolParameter ) ge
Hi Johngui,
Can you open the console in your web browser and look at the url to which
the file was posted to?
Also please take a look into the Galaxy configuration file
(config/galaxy.ini or universe_wsgi.ini) and try to find out to what the
nginx_upload_path is set to.
Thanks,
Sam
On Wed, Nov
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