Re: [galaxy-dev] Problems with planemo functional tests

[Léo Biscassi]

Hi, the command that you suggested not working, the same output is
presented. I tested with the following commands:

*sudo planemo test
/home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml
--galaxy_root=/home/leobiscassi/programs/galaxy*

*sudo planemo test
/home/leobiscassi/programs/galaxy/tools/planemo-tutorial/seqtk_seq.xml*

What is the influence of xUnit file in the process? I did the question
because the warning message showing "*Cannot locate xUnit report option for
tests - update Galaxy for more detailed breakdown*".

P.S.: My Galaxy instance is the latest stable version.

Best regards,

On Thu, Mar 3, 2016 at 2:53 AM Björn Grüning 
wrote:

> Hi,
>
> maybe I'm mistaken something, its way to early here ... but you need to
> specify a path to the tool you want to test.
>
> For example:
>
> planemo test /foo/bar/foo.xml
>
> or to a directory full of tools.
>
> planemo test /foo/bar
>
> Hope this helps,
> Bjoern
>
> Am 03.03.2016 um 04:48 schrieb Léo Biscassi:
> > Hi Folks,
> > I tried follow this tutorial [1], but I have problems in execute the
> > command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for
> > perform functional tests, any suggestion?
> > Bellow some images about this problem:
> >
> > imagem1.jpg
> > *Figure 1: *Command
> >
> > imagem2.jpg
> > *Figure 2:* Error
> >
> > imagem3.jpg
> > *Figure 3: *Galaxy Path
> >
> > Planemo's version is 0.23.0.
> >
> > [1] https://planemo.readthedocs.org/en/latest/writing_standalone.html
> >
> > P.S: The command is utilized for same tool presented in tutorial.
> >
> > Att.
> > --
> > *Léo Biscassi*
> > Facebook - https://pt-br.facebook.com/lbiscassi
> > Linkedin - https://br.linkedin.com/in/leobiscassi
> > Skype - biscassi.leo
> > Twitter - https://twitter.com/leobiscassi
> >
> >
> > ___
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> >
>
-- 
*Léo Biscassi*
Facebook - https://pt-br.facebook.com/lbiscassi
Linkedin - https://br.linkedin.com/in/leobiscassi
Skype - biscassi.leo
Twitter - https://twitter.com/leobiscassi
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[galaxy-dev] Problems with planemo functional tests

[Léo Biscassi]

Hi Folks,
I tried follow this tutorial [1], but I have problems in execute the
command "planemo t --galaxy_root=/home/leobiscassi/programs/galaxy" for
perform functional tests, any suggestion?
Bellow some images about this problem:

[image: imagem1.jpg]
*Figure 1: *Command

[image: imagem2.jpg]
*Figure 2:* Error

[image: imagem3.jpg]
*Figure 3: *Galaxy Path

Planemo's version is 0.23.0.

[1] https://planemo.readthedocs.org/en/latest/writing_standalone.html

P.S: The command is utilized for same tool presented in tutorial.

Att.
-- 
*Léo Biscassi*
Facebook - https://pt-br.facebook.com/lbiscassi
Linkedin - https://br.linkedin.com/in/leobiscassi
Skype - biscassi.leo
Twitter - https://twitter.com/leobiscassi
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Re: [galaxy-dev] Galaxy on Azure

[Alex Lenail]

Thanks! I ended up using Bjoern's Docker implementation
.

On Mon, Feb 29, 2016 at 6:49 PM, Enis Afgan  wrote:

> Hi Alex,
> Assuming you'd want to set it up as a dedicated server on a VM running on
> Azure, I'd suggest taking a look at the production instance setup notes:
> https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
>
> Other admin topics are also available on the wiki:
> https://wiki.galaxyproject.org/Admin
>
> Hope this helps.
>
> On Mon, Feb 29, 2016 at 1:40 PM, Alex Lenail  wrote:
>
>> Hello,
>>
>> My name is Alex LeNail and I'm a researcher at MIT. I'm looking to set up
>> a Galaxy server, and our lab has a great deal of Microsoft Azure credits,
>> so we were hoping to deploy Galaxy on there.
>>
>> Where should I start if I wanted to set that up? I haven't really found
>> any resources online with any description of how that might be
>> accomplished.
>>
>> Thanks,
>>
>> --Alex
>>
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Re: [galaxy-dev] workflows "show in menu" by default

[John Chilton]

There is no option to enable this automatically. There is not ability
to modify this via the API (though I created an issue here
https://github.com/galaxyproject/galaxy/issues/1842).

I guess what I would do to implement this is to refactor places where
trans.user.stored_workflow_menu_entries is read specifically to use a
new method - like trans.users_stored_workflow_menu_entries(). Then add
a config option that just swapped this to read non-deleted workflows
of the user instead of the explicitly marked ones. I'd +1 a clean
implementation of that if you have some available developer time to
take a crack at that. If there isn't time to work on it but others
think it would be useful, I'd encourage creating an issue for this -
https://github.com/galaxyproject/galaxy/issues/new.

-John

On Tue, Mar 1, 2016 at 1:19 PM, Cameron Jack  wrote:
> Hi all,
>
>
> In the /workflow/configure_menu screen there is an tickbox option for each
> installed workflow to "show in menu". Is there a way I could enable this by
> default, or in code via bioblend  (couldn't see any hint of this in the
> docs)? Perhaps I could extend bioblend to do this?
>
>
> Cheers,
>
> Cam
>
>
> Cameron Jack
>
> Acting Manager & Bioinformatician
> ANU Bioinformatics Consultancy
> The Australian National University
>
> The John Curtin School of Medical Research
> Building 131 Garran Road
> Acton 0200, ACT
>
> Ph (office): +61 2 612 51128
> Ph (mobile): +61 4 2368 0745
> Email: cameron.j...@anu.edu.au
> Group email: a...@anu.edu.au
>
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Re: [galaxy-dev] Dependencies for sudo scripts/drmaa_external_runner.py ?

[Peter Cock]

On Wed, Mar 2, 2016 at 5:27 PM, Nate Coraor  wrote:
> On Wed, Mar 2, 2016 at 12:07 PM, Peter Cock 
> wrote:
>>
>> On Wed, Mar 2, 2016 at 4:59 PM, Nate Coraor  wrote:
>> > On Mon, Feb 29, 2016 at 12:10 PM, Peter Cock 
>> > wrote:
>> >>
>> >> Hello all,
>> >>
>> >> QUESTION: When submitting jobs to the cluster as the real user,
>> >> how should sudo scripts/drmaa_external_runner.py be told which
>> >> Python to use, and how would it activate the venv if needed for
>> >> the DRMAA dependency?
>> >
>> >
>> > Hi Peter,
>> >
>> > I think the easiest solution to this is probably to write a wrapper
>> > script
>> > that sets up the environment for drmaa_external_runner.py and call this
>> > wrapper (with the same args), which can then pass the args to
>> > drmaa_external_runner.py.
>> >
>> > --nate
>>
>> Thanks Nate,
>>
>> So we'd write a shell script called drmaa_external_runner.py which
>> setups the Python environment and then calls a copy of the original
>> Python script drmaa_external_runner.py - has anyone else tried this?
>
>
> The name of the run job script to call is controlled by the
> drmaa_external_runjob_script variable in galaxy.ini:
>
> https://github.com/galaxyproject/galaxy/blob/dev/config/galaxy.ini.sample#L1073
>
> Here you can change this to your wrapper.

Thanks Nate - I should have realised this was a configuration option.

>> Clearly using Python 2.7 on a system with a Python 2.6 default (CentOS 6)
>> is part of the problem. Maybe we can just install the Python DRMAA under
>> the system Python 2.6 instead?
>
> This part would work, but wouldn't you still need the environment variables
> to be set?
>
> --nate

Good point. The custom script option with hard coded environment variables
sounds more straightforward that fighting the Linux OS settings.

Peter
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Re: [galaxy-dev] Galaxy 15.10 Jobs not running

[Nate Coraor]

On Tue, Mar 1, 2016 at 1:19 PM, Ryan G  wrote:

> Hi all - We recently merged in Galaxy 15.10 changes into our staging
> instance and have noticed jobs are no longer dispatched.  There is no
> obvious problem in the log file.
>
> I see in github, commits have recently been made to revert something, but
> I'm not clear what.
>
> Is there something going on with the job runner?  Better yet, how can I
> track down what my issue is?
>

Hi Ryan,

There aren't any current issues with job running that I'm aware of.
Typically the first thing to check is your job_conf.xml and make sure that
handlers defined are the same as handlers (with matching server names) that
you are starting). The log for your handlers should show them loading the
job_conf.xml and setting up job plugins if they are identified as handlers
in the config.

--nate


>
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Re: [galaxy-dev] Load tools without service interruption

[John Chilton]

Hans is correct prior to Galaxy 16.01. The 16.01 release of Galaxy
added a monitor attribute to config/tool_conf.xml.sample (e.g.
) that causes Galaxy to watch that file for
changes and reload the toolbox on modifications. No need to add this
to tool shed tool confs (and it would probably break them) but for
non-tool shed tool confs this should work.

Additionally, the toolbox tool conf can have a  element that will cause Galaxy to load a whole
directory at a time - this can be combined with active monitoring and
reloading of modified tools  in that directory by installing
"watchdog" ($GALAXY_ROOT/.venv/bin/pip install watchdog) into Galaxy's
virtualenv and then setting watch_tools=True in galaxy.ini. This is
what planemo machine does to monitor a directory of tools (there have
been reports that this approach may be a bit buggy - help with bug
reports and/or fixes would be appreciated).

-John


On Wed, Mar 2, 2016 at 8:32 AM, Hans-Rudolf Hotz  wrote:
> Hi Floreline
>
>
> It depends on the 'source' of the tool:
>
> If you add the tool via Tool Shed, then there is no need to restart the
> Galaxy server. However, if you add a tool manually (i.e. by adding a line to
> tool_conf.xml) you need to restart the server - at least that is my current
> knowledge.
>
>
> Hans-Rudolf
>
>
>
> On 03/01/2016 11:09 PM, Floreline TOUCHARD wrote:
>>
>> Hi Galaxy team,
>>
>> Is there a way to add a tool without service interruption ?
>> Something like a "sh run.sh --reload" (not "restart") command.
>> I think I saw this information once, but I can't put my hand on it
>> anymore.
>>
>> Thanks in advance !
>> F.T
>>
>>
>>
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>>
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Re: [galaxy-dev] Docker tools

[Björn Grüning]

Hi Abdulrahman,

this does not belong to a tool, this is more a configuration for an
admin. The tools does not care where it runs.

So what you need to do is to set up a job destination and configure your
tools to use this destination.

Here is a small documentation about it:

https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L227

The skype meeting today at 3.00 sounds good!
Cheers,
Bjoern


Am 02.03.2016 um 09:55 schrieb Abdulrahman Azab:
> Hi Galaxy,
> 
> 
> I'm working on a project for running galaxy on the top of a docker swarm
> cluster. The docker tag in the tool xml so far supports access only to
> the local docker host. To submit to the swarm manager, the command
> should be:
> 
> 
> $ docker -H tcp://: run ...
> 
> instead of:
> 
> $ docker run ...
> 
> 
> Is it possible to add an xml tag attribute to support that option?
> 
> This would off course require that all files are located in a shared
> file-system.
> 
>  
> 
> Thank you,
> 
> Yours sincerely,
> Abdulrahman Azab
> 
> Head engineer
> ELIXIR.NO, Genomic Hyperbrowser Team  
> Research Group for Biomedical Informatics, Department of Informatics (IFI) 
> Research Support Services Group, University Center for Information
> Technology (USIT)
> University of Oslo, Boks 1072 Blindern, NO-0316 OSLO, Norway
> Email: a...@ifi.uio.no, a...@usit.uio.no
> Cell-phone: +47 46797339
> 
> Senior Lecturer in Computer Engineering
> Faculty of Engineering, University of Mansoura, 35516-Mansoura, Egypt
> Email: abdulrahman.a...@mans.edu.eg
> 
> 
> 
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Re: [galaxy-dev] Docker tools

[Marius van den Beek]

Hello Abdulrahman,

I believe you can control the docker host in the job_conf.xml.
https://github.com/galaxyproject/galaxy/blob/dev/config/job_conf.xml.sample_advanced#L227
I haven't' tried this yet, but it seems that it should work.

Cheers,
Marius

On 2 March 2016 at 09:55, Abdulrahman Azab  wrote:

> Hi Galaxy,
>
>
> I'm working on a project for running galaxy on the top of a docker swarm
> cluster. The docker tag in the tool xml so far supports access only to the
> local docker host. To submit to the swarm manager, the command should be:
>
>
> $ docker -H tcp://: run ...
>
> instead of:
>
> $ docker run ...
>
>
> Is it possible to add an xml tag attribute to support that option?
>
> This would off course require that all files are located in a shared
> file-system.
>
>
> Thank you,
>
> Yours sincerely,
> Abdulrahman Azab
>
> Head engineer
> ELIXIR.NO, Genomic Hyperbrowser Team
> Research Group for Biomedical Informatics, Department of Informatics (IFI)
> Research Support Services Group, University Center for Information
> Technology (USIT)
> University of Oslo, Boks 1072 Blindern, NO-0316 OSLO, Norway
> Email: a...@ifi.uio.no, a...@usit.uio.no
> Cell-phone: +47 46797339
> 
> Senior Lecturer in Computer Engineering
> Faculty of Engineering, University of Mansoura, 35516-Mansoura, Egypt
> Email: abdulrahman.a...@mans.edu.eg
> 
>
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[galaxy-dev] Fwd: BOSC 2016 Call for Abstracts

[Peter Cock]

Dear all,

As BOSC co-chair I would like to encourage you all to think about
attending BOSC 2016, and if you are working on your own open
source software for bioinformatics please consider submitting an
abstract. See the email below and:

http://news.open-bio.org/2016/03/01/bosc-2016-call-for-abstracts/

We've had lots of Galaxy related talks at BOSC over the years,
and look forward to more abstract submissions from the Galaxy
community this year as well.

Also, as a member of the Open Bioinformatics Foundation (OBF)
Board of Directors, I am delighted to let you know about the new
OBF Travel Fellowship which could be used to attend BOSC, or
the Galaxy Community Conference (GCC2016) if your work fits:

http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/

Thank you,

Peter
[Galaxy contributor & tool developer, BOSC co-chair,
OBF Secretary, etc.]

P.S. In case you missed the earlier announcement last year, we
finally got rid of the paper forms for OBF membership, see:

http://news.open-bio.org/2015/12/10/online-membership-form/



-- Forwarded message --
From: Peter Cock 
Date: Tue, Mar 1, 2016 at 5:56 PM
Subject: BOSC 2016 Call for Abstracts
To: bosc-annou...@lists.open-bio.org
Cc: bosc-review...@lists.open-bio.org, "b...@open-bio.org" 


Call for Abstracts for the 17th Annual Bioinformatics Open Source
Conference (BOSC 2016), a Special Interest Group (SIG) of ISMB 2016.

Dates: July 8-9, 2016
Location: Orlando, FL
Web site: http://www.open-bio.org/wiki/BOSC_2016
Email: b...@open-bio.org
BOSC announcements mailing list:
http://lists.open-bio.org/mailman/listinfo/bosc-announce
Twitter: @OBF_BOSC and @OBF_News

Important Dates:

 * Call for one-page abstracts opens: March 1, 2016
 * Abstract submission deadline: April 1, 2016
 * Travel fellowship application deadline: April 15, 2016
 * Authors notified: May 6, 2016
 * Codefest 2016: July 6-7, 2016, Orlando, FL (confirming venue)
 * BOSC 2016: July 8-9, 2016, Orlando, FL
 * ISMB 2016: July 8-12, 2016, Orlando, FL

The Bioinformatics Open Source Conference (BOSC) is run as a two-day
meeting before the annual ISMB conference. It is organized by the Open
Bioinformatics Foundation (OBF), a non-profit group dedicated to
promoting the practice and philosophy of open source software
development and open science within the biological research community.
BOSC offers a focused environment for developers and users to interact
and share ideas about standards; software development practices;
practical techniques for solving bioinformatics problems; and
approaches that promote open science and sharing of data, results and
software.

We welcome one-page abstracts on any topic of relevance to open source
bioinformatics and open science. Presentation formats are lightning
talks, longer talks, and/or posters. We plan to offer a limited number
of travel fellowships to help offset expenses for some accepted
speakers who would not otherwise be able to attend BOSC – please see
the OBF Travel Fellowship announcement for more information:

http://news.open-bio.org/2016/03/01/obf-travel-fellowship-program/

Session topics include:
 * Open Science and Reproducible Research
 * Standards and Interoperability
 * Data Science
 * Visualization
 * Translational Bioinformatics
 * Bioinformatics Open Source Libraries and Projects

If your company or organization is interested in helping to sponsor
BOSC 2016, please contact us! Sponsors in 2015 included Google,
GigaScience, Curoverse and Bina – we thank them for their support.

Please see http://www.open-bio.org/wiki/BOSC_Abstract_Submission for
abstract submission instructions,

Thank you,

BOSC 2016 Organizing Committee:
Nomi Harris and Peter Cock (co-chairs), Brad Chapman, Christopher
Fields, Karsten Hokamp, Hilmar Lapp, Mónica Muñoz-Torres, Heather
Wiencko
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[galaxy-dev] Docker tools

[Abdulrahman Azab]

Hi Galaxy,


I'm working on a project for running galaxy on the top of a docker swarm 
cluster. The docker tag in the tool xml so far supports access only to the 
local docker host. To submit to the swarm manager, the command should be:


$ docker -H tcp://: run ...

instead of:

$ docker run ...


Is it possible to add an xml tag attribute to support that option?

This would off course require that all files are located in a shared 
file-system.



Thank you,

Yours sincerely,
Abdulrahman Azab

Head engineer
ELIXIR.NO, Genomic Hyperbrowser Team
Research Group for Biomedical Informatics, Department of Informatics (IFI)
Research Support Services Group, University Center for Information Technology 
(USIT)
University of Oslo, Boks 1072 Blindern, NO-0316 OSLO, Norway
Email: a...@ifi.uio.no, a...@usit.uio.no
Cell-phone: +47 46797339

Senior Lecturer in Computer Engineering
Faculty of Engineering, University of Mansoura, 35516-Mansoura, Egypt
Email: 
abdulrahman.a...@mans.edu.eg
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Re: [galaxy-dev] Load tools without service interruption

[Hans-Rudolf Hotz]

Hi Floreline


It depends on the 'source' of the tool:

If you add the tool via Tool Shed, then there is no need to restart the 
Galaxy server. However, if you add a tool manually (i.e. by adding a 
line to tool_conf.xml) you need to restart the server - at least that is 
my current knowledge.



Hans-Rudolf


On 03/01/2016 11:09 PM, Floreline TOUCHARD wrote:

Hi Galaxy team,

Is there a way to add a tool without service interruption ?
Something like a "sh run.sh --reload" (not "restart") command.
I think I saw this information once, but I can't put my hand on it anymore.

Thanks in advance !
F.T



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Re: [galaxy-dev] Galaxy External Authentication and API access

[Hans-Rudolf Hotz]

Hi Lance

just double checking: Have you implemented this fix:

https://github.com/galaxyproject/galaxy/pull/1003
(https://gist.github.com/8d0412367371127e90ad)

This solved our problem with the 'View all histories' nicely - though we 
still have problems with 'Impersonate a user'



Regards, Hans-Rudolf


On 03/01/2016 11:06 PM, Lance Parsons wrote:

I am currently using Apache and CAS
(https://en.wikipedia.org/wiki/Central_Authentication_Service) to
provide external authentication to Galaxy. I'd like to start using the
API, however, I've not been able to find a way to get that to work.

A while back, someone suggested using the following:


 Satisfy Any
 Allow from all


However, this breaks the history view at least, since the ajax call is
an /api call and no HTTP_REMOTE_USER gets set. Does anyone have any
suggestions? I'd love to get this going with some simple configuration...

I know I could move over to LDAP, but that is not desirable since it's
less secure than CAS.

Another option would be to implement CAS within Galaxy, but that does
seem like a good bit of work, but perhaps someone is already working on
it or at least interested?



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