This is the page describing the xml syntax that can be used to wrap tools.
If its not on this page I would guess that you can't use it in your xml
code.
https://docs.galaxyproject.org/en/latest/dev/schema.html
On Mon, Feb 20, 2017 at 5:22 AM, Jochen Bick
wrote:
> Hi
b/dev/
> config/job_metrics_conf.xml.sample
>
> I've never used it, but perhaps the backend using Collectl
> (http://collectl.sourceforge.net/) would cover this?
>
> Peter
>
> On Fri, Jan 27, 2017 at 2:50 PM, Katherine Beaulieu
> <katherine.beaulieu...@gmail.com>
mail).
>
> Peter
>
> On Thu, Jan 26, 2017 at 6:58 PM, Katherine Beaulieu
> <katherine.beaulieu...@gmail.com> wrote:
> > Hi there,
> > We are trying to build our own Galaxy cluster and I was wondering if
> there
> > was a way to check if there are any run
Hi there,
We are trying to build our own Galaxy cluster and I was wondering if there
was a way to check if there are any running Galaxy jobs on a specific
server? This would be to determine whether or not to remove the server from
the cluster.
Thanks!
Katherine
Hi Everyone,
Does anyone know how execution of code files happens? Is there a function
somewhere that fills the parameters in?
Cheers,
Katherine
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in your mail client. To manage your
ernals so it'll take some time
> and understanding of the process to get it done. Feel free to email with
> any questions.
>
>
>
> On Tue, Nov 8, 2016 at 1:31 PM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>> Hi Galaxy Community,
>> Do
-- Forwarded message --
From: Katherine Beaulieu <katherine.beaulieu...@gmail.com>
Date: Mon, Oct 24, 2016 at 2:55 PM
Subject: Re: [galaxy-dev] Workflow Execution Files
To: Aysam Guerler <aysam.guer...@gmail.com>
Awesome thanks Aysam! I was wondering if you know
Hi Everyone,
Does anyone know what files workflow execution goes through? I had assumed
it just went through the same files as individual jobs for each step but I
don't think that's the case. I was looking at tool-form.js but it doesn't
seem to be executing that file.
Thanks!
Katherine
Hi Steve,
In terms of accessing the user's api key within a tool definition file,
have a look at this thread I had started. John had suggested something but
I haven't gotten it to work but maybe you will have more luck than me.
Hello Galaxy Community,
Is it possible to get the job_id listed on the info 'eye' page within a
tool wrapper?
Katherine
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and hack on that pattern.
>
> The are a lot of examples in the code of using sqlalchemy - if you
> want an example of like using postgres directly - here is one:
>
> https://github.com/galaxyproject/galaxy/blob/dev/scripts/cleanup_datasets/
> pgcleanup.py
>
> -John
>
&
, 2016 at 9:07 PM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
>
>
> On Fri, Sep 2, 2016 at 9:07 PM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>> Hi Bjorn,
>> Thank you for taking the time to reply to my question. I don't th
Hi Everyone,
I am looking to set up a web server and handler process for galaxy within a
virtual machine. I've tried following the instructions written here:
https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling#Starting_and_Stopping
But, I can still start Galaxy with sh run.sh, also the
On Fri, Sep 2, 2016 at 9:07 PM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Hi Bjorn,
> Thank you for taking the time to reply to my question. I don't think this
> quite fits what I am trying to accomplish. I am trying to pass a set of
> metadata key value pai
On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Hi Peter,
> The code file tag is generally used in populating select lists. So
> basically you have a function from a code file that is loaded before
> runtime of the tool and you ca
Hello Galaxy Community,
I was wondering if anyone had ever come across a situation where they have
had to pass the contents of a repeat parameter to a code file in a Galaxy
tool config? Is there any way to do this?
Katherine
___
Please keep
Hi Galaxy Community,
Does anyone know if it is possible to run a tool in batch mode if there is
no data type parameter in the tool? I'd love to be able to run a tool in
batch mode based on a multiple select list instead.
Katherine
___
Please
ugh you'll need to find the
> correct job ID from the 'job' table.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
Hi everyone,
Does anyone know where parameters are being retrieved from the database
during tool execution within Galaxy's files. I am trying to change a value
in the database after the value has been retrieved.
Thanks!
Katherine
___
Please
erent than e.g. user specified
> downsampling amounts. or library names, etc.
> I have tools that accept many of these.
>
>
> Brad
>
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
>
>
>
> On Aug 26, 2016, at 10:57 AM, Katherine Beaulie
ed, etc)
>
>
> Brad
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
>
>
>
> On Aug 26, 2016, at 10:42 AM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>
>
> On Fri, Aug 26, 2016 at 10:42 AM, Kat
On Fri, Aug 26, 2016 at 10:42 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Hi Peter,
> I think I did not explain myself well. I meant that if I have a tool that
> takes multiple file paths and outputs multiple Galaxy datasets to the
> history, would thi
Hi Everyone,
Would anyone be able to tell me the conditions which would make a tool
non-workflow compatible? I have a tool that imports files from a third
party application and auto-detects the file format. There is also the
option to upload multiple files at once so the tool always uploads at
On Thu, Aug 25, 2016 at 2:25 PM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Hi Peter,
> No actually I meant in what file is the table job_parameter getting filled
> during execution?
> Katherine
>
> On Fri, Aug 5, 2016 at 3:00 PM, Peter van Heusden
Hi everyone,
We are trying to obtain the three things in the tile of this post to enable
a tool to use the bioblend api and get the .ga file so that any user can go
back into our system, get the workflow associated with the end file, get
the input parameters which are tags associated with the end
Would anyone be able to tell me in what file the storing of tool parameters
into the database occurs?
Thanks!
Katherine
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Hi everyone,
I was wondering if anyone knew how to pass the url of your galaxy instance
to a tool as well as a way to authenticate so I could use the bioblend api
within my tool?
Thanks,
Katherine
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On Wed, Aug 3, 2016 at 11:36 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Ok thanks for the information!
>
> On Wed, Aug 3, 2016 at 11:21 AM, Eric Rasche <e...@tamu.edu> wrote:
>
>> Hi Katherine,
>>
>> There is unfortunately no di
On Wed, Aug 3, 2016 at 11:35 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Generally what I've found is that you have to go to another html page and
> in that page's html code you have to specify to go back to galaxy and your
> tool wrapper should take car
Hi Everyone,
I know this is sort of a controversial topic so I will try to tread
lightly. It seems that for a couple of years the idea of a password
parameter for Galaxy tools has come up a lot but has also been rejected a
lot although I believe there is a lot of merit to it. I have found at least
h fills this template:
> https://github.com/galaxyproject/galaxy/blob/dev/templates/show_params.mako
>
> On Wed, Jul 27, 2016 at 1:20 PM Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>> Hello Galaxy Community,
>> Does anyone know what file wo
gt; the codebase with grep at the command line (also searching
>> directly on GitHub works pretty well) trying to trace functionality
>> when I was debugging something.
>>
>> Hopefully one of the Galaxy developers will be able to answer.
>>
>> Peter
>&
Dear all,
I am looking for the files/functions that get called from the point where
you click on the tool name to the point where you get an html version of
your tool on the screen. Could someone indicate what this path looks like?
I would be really appreciative!
Thanks,
Katherine
Well I guess this didn't reply to the post I wanted, sorry everyone!
On Mon, Jul 18, 2016 at 6:50 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Hi there,
> I have developed a tool that does the importing and exporting to Galaxy.
> Please see the attached lin
Hi there,
I have developed a tool that does the importing and exporting to Galaxy.
Please see the attached link to the github repos for the two tools.
Please keep in mind that this tool is still in development. As well, it has
only been tested on a local instance of Galaxy and the authentication
Hi everyone,
I am looking to implement a new parameter type for galaxy tool development.
Does anyone know what would be involved in doing something like this or
perhaps what files would need to be edited?
___
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Actually just figured out the history content api id, just needing the
extra stuff about the job like runtime and start and end times.
On Fri, Jul 8, 2016 at 8:55 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:
> Hi Greg,
> Thanks for the link to your githu
tool
> will generate metadata for some different tool that has already been
> executed.
>
> Here is an example of a basic command line in one of these tool configs
> that will provide the job stuff to the underlying script.
>
>
>
>
>
> Cheers!
Hi everyone,
I am working on a tool which attempts to create a file which stores all the
metadata associated with a job execution. The things I know how to access
right now are the file extension, name history id, dataset id. I'd like to
know how to access other things like the job id, uuid, file
appreciated.
On Thu, Jun 30, 2016 at 1:01 PM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:
> Maybe sharing your tool XML file would be best - is it on GitHub?
>
> Peter
>
> On Wed, Jun 29, 2016 at 7:43 PM, Katherine Beaulieu
> <katherine.beaulieu...@gmail.com> wrote:
&g
ide
> of Galaxy to confirm that works?
>
> If Galaxy wrongly picks another fileformat, check where
> in the datatypes_conf.xml is your file format listed? The
> order the sniffing functions are run is important.
>
> Peter
>
> On Wed, Jun 29, 2016 at 3:56 PM, Kathe
Hi everyone,
I am looking to auto-detect the file format of a file outputted by a python
tool I have written. Does anyone have any idea how to do this? I have tried
setting the format attribute to "auto" with no luck. Let me know if you
would like to see my tool config file.
Cheers,
Katherine
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