[galaxy-dev] Load tools without service interruption

[Floreline TOUCHARD]

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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[galaxy-dev] Galaxy External Authentication and API access

[Lance Parsons]

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?



--
Lance Parsons - Scientific Programmer
Carl C. Icahn Laboratory - Room 141 (Temporary)
Lewis-Sigler Institute for Integrative Genomics
Princeton University

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Re: [galaxy-dev] Alternative methods for external authentication

[Eric Rasche]

Hi Amelia,

The authentication system was re-worked within the past year to a
pluggable module system. There is a reference LDAP

implementation that does not use Apache at all, as well as a few other
examples like pam authentication in the same folder. I'm sure you could
extend this to talk to any other auth system you may wish to use.

If you write your own, you can load the module in the auth_conf.xml

file.

Cheers,
Eric

On 03/01/2016 07:26 PM, Amelia Ireland wrote:
> I'd like to set up a galaxy instance to use a custom external
> authentication system. The documentation has examples of using LDAP
> and Apache-based authentication, but I wondered if there was a more
> general method for hooking up a login system.
>
> Thanks!
>
> Amelia Ireland
> Integrated Microbial Genomics
>
>
>
> ___
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-- 
--
Eric Rasche
Programmer II

Center for Phage Technology
Rm 312A, BioBio
Texas A University
College Station, TX 77843
404-692-2048 
e...@tamu.edu 
Not responding quickly enough?

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[galaxy-dev] Alternative methods for external authentication

[Amelia Ireland]

I'd like to set up a galaxy instance to use a custom external
authentication system. The documentation has examples of using LDAP and
Apache-based authentication, but I wondered if there was a more general
method for hooking up a login system.

Thanks!

Amelia Ireland
Integrated Microbial Genomics
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Re: [galaxy-dev] Missing modules after upgrade to 16.01

[Nate Coraor]

Hi Cristian,

It's up to you whether you keep it with Galaxy or not. I prefer not to
modify the Galaxy clone at all so I keep it outside. More details about
keeping the virtualenv separate can be found here in the documentation:


https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#managing-dependencies-manually

--nate

On Tue, Mar 1, 2016 at 1:40 PM, C. Ch.  wrote:

> Hi Bjoern,
>
> Thanks for the tip! My problem was that galaxy assumes that the venv is in
> the installation directory as a hidden folder whilst I have the virtual
> environment installed at ~/venv and configured in my .bashrc to launch at
> login. Why I installed it like that? I don't remember... Probably to
> separate the venv from the galaxy installation.
>
> For the future, is it better to change my venv to reside in the galaxy
> folder or is it of no importance where I keep it?
>
> Thanks again!
> Cristian
>
> > Subject: Re: [galaxy-dev] Missing modules after upgrade to 16.01
> > To: tuto...@hotmail.com; galaxy-dev@lists.galaxyproject.org
> > From: bjoern.gruen...@gmail.com
> > Date: Tue, 1 Mar 2016 13:47:41 +0100
> >
> > Hi,
> >
> > please have a look at this script and run it:
> >
> > ./scripts/common_startup.sh
> >
> > Also make sure you have samtools installed.
> >
> > Ciao,
> > Bjoern
> >
> > Am 01.03.2016 um 13:39 schrieb C. Ch.:
> > > Hi,
> > >
> > > I've upgraded to 16.01 and have error messages indicating missing
> > > modules. This produces problems while setting the metadata. The
> > > processes run, the results are there but the history entry is in red.
> > >
> > > How can I trigger the installation of all the modules that galaxy needs
> > > with the new pip based mechanism?
> > >
> > > Thanks for the help!
> > > Cristian
> > >
> > >
> > > ___
> > > Please keep all replies on the list by using "reply all"
> > > in your mail client. To manage your subscriptions to this
> > > and other Galaxy lists, please use the interface at:
> > > https://lists.galaxyproject.org/
> > >
> > > To search Galaxy mailing lists use the unified search at:
> > > http://galaxyproject.org/search/mailinglists/
> > >
>
> ___
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Re: [galaxy-dev] Missing modules after upgrade to 16.01

[C. Ch.]

Hi Bjoern,
Thanks for the tip! My problem was that galaxy assumes that the venv is in the 
installation directory as a hidden folder whilst I have the virtual environment 
installed at ~/venv and configured in my .bashrc to launch at login. Why I 
installed it like that? I don't remember... Probably to separate the venv from 
the galaxy installation.
For the future, is it better to change my venv to reside in the galaxy folder 
or is it of no importance where I keep it?
Thanks again!Cristian

> Subject: Re: [galaxy-dev] Missing modules after upgrade to 16.01
> To: tuto...@hotmail.com; galaxy-dev@lists.galaxyproject.org
> From: bjoern.gruen...@gmail.com
> Date: Tue, 1 Mar 2016 13:47:41 +0100
> 
> Hi,
> 
> please have a look at this script and run it:
> 
> ./scripts/common_startup.sh
> 
> Also make sure you have samtools installed.
> 
> Ciao,
> Bjoern
> 
> Am 01.03.2016 um 13:39 schrieb C. Ch.:
> > Hi,
> > 
> > I've upgraded to 16.01 and have error messages indicating missing
> > modules. This produces problems while setting the metadata. The
> > processes run, the results are there but the history entry is in red.
> > 
> > How can I trigger the installation of all the modules that galaxy needs
> > with the new pip based mechanism?
> > 
> > Thanks for the help!
> > Cristian
> > 
> > 
> > ___
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> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
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> > 
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> >   http://galaxyproject.org/search/mailinglists/
> > 
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[galaxy-dev] March 2016 Galaxy News: GCC2016 deadlines this month, GSOC 2016, RAD-Seq Hack …

[Dave Clements]

Hello all,

The *March 2016 Galactic News
* is hot off the
presses:

   -

   *GCC2016 *
news:
   -

  *Oral presentation abstracts due March 20
  
.*
If
  you are doing work in data-intensive biology then you are strongly
  encourage to present your work at the conference. Oral presentations,
  poster presentations, and the new Visualization Showcase & Software Demos
  are all opportunities to share your work.
  -

  Register early
  

and
  save up to 40% off regular registration costs. Early bird prices start at
  less than $45 / day for post-docs and students.
  -

  Apply for a GCC2016 Scholarship
  

  . *Applications from international applicants are due March 20.*
  -

  The 2016 GMOD Meeting
  

will
  be held immediately following GCC2016, also at Indiana University.
  -

  And, we have a returning sponsor: Please welcome *BioTeam
  * to
  GCC2016.
  -

   *March 7-8: Online IUC Contribution Fest - RADSeq Tools and Workflows
   
*
   -

   *Galaxy in Google Summer of Code
   
*
   -

   Twelve other upcoming events
   
   -

   54 new publications, including 4 highlighted pubs
   
   -

   New jobs
   
   -

   New releases
   ,
   including the new CloudBridge
    and
   two important security announcements
   
   -

   Two new Galaxy servers
   

   -

   New ToolShed Contributions
   

Dave Clements and the Galaxy Team


-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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Re: [galaxy-dev] tmp directory

[Nicola Soranzo]

You can use tmpwatch on RedHat/CentOS/Fedora or tmpreaper on Debian/Ubuntu.

Cheers,
Nicola

On 01/03/16 14:30, Raphenya, Amogelang wrote:

Is there a script that is used to clean up database/tmp

/
/   
/*Amos Raphenya* /
/Bioinformatics Software Developer/
/Department of Biochemistry & Biomedical Sciences/
/McMaster University, MDCL //2317/
/p: (905) 525-9140//ext: //22787/
/a:1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1/
/e: raphe...@mcmaster.ca  /
/skype:amos_raphenya/


On Feb 29, 2016, at 10:21 AM, Björn Grüning 
> wrote:


Hi,

if you are not overwriting this value with a object_store setting, it
defaults to 'database/tmp' as written in galaxy.ini. The values are the
default values which you see.

Ciao,
Bjoern

Am 29.02.2016 um 16:19 schrieb Raphenya, Amogelang:

Hi All,

Where are the temporary files stored if the line below is commented out?

|# Temporary files are stored in this directory. new_file_path =
database/tmp|


Thank you.

/
/
/*Amos Raphenya* /
/Bioinformatics Software Developer/
/Department of Biochemistry & Biomedical Sciences/
/McMaster University, MDCL //2317/
/p: (905) 525-9140 //ext: //22787/
/a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1/
/e: raphe...@mcmaster.ca  
 /

/skype: amos_raphenya/




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Re: [galaxy-dev] tmp directory

[Raphenya, Amogelang]

Is there a script that is used to clean up database/tmp














Amos Raphenya 
Bioinformatics Software Developer
Department of Biochemistry & Biomedical Sciences
McMaster University, MDCL 2317
p: (905) 525-9140 ext: 22787
a: 1280 Main St W.,Hamilton,
 Ontario, Canada L8S 4K1
e:  raphe...@mcmaster.ca 
skype: amos_raphenya













On Feb 29, 2016, at 10:21 AM, Björn Grüning  wrote:

Hi,

if you are not overwriting this value with a object_store setting, it
defaults to 'database/tmp' as written in galaxy.ini. The values are the
default values which you see.

Ciao,
Bjoern

Am 29.02.2016 um 16:19 schrieb Raphenya, Amogelang:
Hi All,

Where are the temporary files stored if the line below is commented out?

|# Temporary files are stored in this directory. new_file_path =
database/tmp|


Thank you.

/
/ 
/*Amos Raphenya* /
/Bioinformatics Software Developer/
/Department of Biochemistry & Biomedical Sciences/
/McMaster University, MDCL //2317/
/p: (905) 525-9140 //ext: //22787/
/a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1/
/e:  raphe...@mcmaster.ca  /
/skype: amos_raphenya/




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[galaxy-dev] workflows "show in menu" by default

[Cameron Jack]

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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[galaxy-dev] GATK problems with data manager

[Scott Szakonyi]

Hi all,

Sorry to be repetitive, but this issue is really blocking our efforts to
develop the workflow that we need in our instance of Galaxy. If anyone has
any familiarity with the issue described below, please let me know. I
really need to get this solved.

One of my co-administrators is having some issues with data
indexed/processed with data managers in GATK. His email to me:


Currently there is no way to load a genome into versions of GATK above
version 1.4.  No version seems to be able to load a reference from history
and only version 1.4 seems to work with the available picard-gatk data
manager.  We need to be able to work with these later versions of GATK, 3.4
on the Galaxy tool shed is the latest.


Thanks!

Scott
-- 
Scott B. Szakonyi
Research Programmer

*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
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Re: [galaxy-dev] Missing modules after upgrade to 16.01

[Björn Grüning]

Hi,

please have a look at this script and run it:

./scripts/common_startup.sh

Also make sure you have samtools installed.

Ciao,
Bjoern

Am 01.03.2016 um 13:39 schrieb C. Ch.:
> Hi,
> 
> I've upgraded to 16.01 and have error messages indicating missing
> modules. This produces problems while setting the metadata. The
> processes run, the results are there but the history entry is in red.
> 
> How can I trigger the installation of all the modules that galaxy needs
> with the new pip based mechanism?
> 
> Thanks for the help!
> Cristian
> 
> 
> ___
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> 
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>   http://galaxyproject.org/search/mailinglists/
> 
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[galaxy-dev] Missing modules after upgrade to 16.01

[C. Ch.]

Hi,
I've upgraded to 16.01 and have error messages indicating missing modules. This 
produces problems while setting the metadata. The processes run, the results 
are there but the history entry is in red.
How can I trigger the installation of all the modules that galaxy needs with 
the new pip based mechanism?
Thanks for the help!Cristian  ___
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[galaxy-dev] novoalign in Galaxy

[Peter van Heusden]

Hi there

We're busy integrating novoalign in our local Galaxy - there doesn't seem
to be a tool around for this, but I recall some people saying they were
using (single threaded) novoalign with Galaxy. Does anyone know if tool XML
has already been written? If not, we'll just have to write it.

Peter
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Re: [galaxy-dev] Downgrade tool upload tool

[Makis Ladoukakis]

Thanks a lot Peter and Aysam! The fix worked perfectly!

Regards,
Makis

Date: Mon, 29 Feb 2016 22:18:37 -0500
Subject: Re: [galaxy-dev] Downgrade tool upload tool
From: aysam.guer...@gmail.com
To: p.j.a.c...@googlemail.com
CC: makis4e...@hotmail.com; j...@galaxyproject.org; 
galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

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 
PR. Thanks a lot for reporting this Makis.

On Mon, Feb 29, 2016 at 8:17 AM, Peter Cock  wrote:
Thanks for clarifying Makis,



I think this change is likely due to changes in Galaxy rather than

in the upload tool itself. On our (slightly out of date) Galaxy or the

public server, that URL no longer loads the original tool form -

you get the new drag-and-drop upload interface.



I would guess some of the special case code like this matters:

https://github.com/galaxyproject/galaxy/blob/fe6d22e1a7e4e6d38b15f4128554783765bc69a1/client/galaxy/scripts/mvc/tool/tools.js#L525



Probably Sam (Aysam) can give you more practical advice (CC'd)?



Peter



On Mon, Feb 29, 2016 at 12:29 PM, Makis Ladoukakis

 wrote:

> I am making some clickable buttons in the home page of my instance through a

> java script that is called from the welcome.html file. These buttons

> correspond to my most used tools. For example I have a section like this:

>

> 

> 

> 

>

> 

>  src="feimg/GetData.gif"/>

> 

>  href="http://myserver/galaxy/tool_runner?tool_id=upload1;

> target="_parent"> height=300%/>

>  href="http://myserver/galaxy/library/browse_libraries; target="_parent"> src="feimg/Libraries.gif" width=250% height=300%/>

> 

> 

> 

> 

>   

>

> indicating two buttons one for the upload tool and one for the libraries.

> The libraries button work but when I click on the button for the upload tool

> the webpage just refreshes instead of opening the tool. This worked

> perfectly with the previous version of the upload tool and I was thinking

> how to get it back.

>

> Thank you,

> Makis

>

>

>> Date: Mon, 29 Feb 2016 11:39:26 +

>> Subject: Re: [galaxy-dev] Downgrade tool upload tool

>> From: p.j.a.c...@googlemail.com

>> To: makis4e...@hotmail.com

>> CC: j...@galaxyproject.org; galaxy-...@lists.bx.psu.edu;

>> galaxy-dev@lists.galaxyproject.org

>

>>

>> Hi Makis,

>>

>> The upload tool is a little special in that it is used internally by

>> Galaxy and doesn't entirely behave like a normal tool.

>>

>> What are you trying to achieve by "downgrading" it?

>>

>> Peter

>>

>> On Mon, Feb 29, 2016 at 11:29 AM, Makis Ladoukakis

>>  wrote:

>> > What about if I used a second "tool upload" tool? I took the python

>> > script

>> > from an earlier version and named it upload_old.py and did the same for

>> > the

>> > xml file (upload.xml -> upload_old.xml) while changing the latter to

>> > call

>> > the new python script. Nevertheless when I did that and tried to run it

>> > I

>> > got a popup window with the following error:

>> >

>> > Tool request failed

>> >

>> > Uncaught exception in exposed API method:

>> >

>> >

>> > Is there a way to make this work? Or maybe another workaround?

>> >

>> > Thank you in advance,

>> > Makis

>> >

>> >

>> >

>> > 

>> > From: j...@galaxyproject.org

>> > Date: Fri, 26 Feb 2016 10:22:44 -0800

>> > Subject: Re: [galaxy-dev] Downgrade tool upload tool

>> > To: makis4e...@hotmail.com

>> > CC: galaxy-...@lists.bx.psu.edu; galaxy-dev@lists.galaxyproject.org

>> >

>> >

>> > Hello,

>> >

>> > The Upload tool is a direct component of Galaxy. To use an earlier

>> > version

>> > of the tool, I believe that you would have to run an earlier version of

>> > Galaxy.

>> >

>> > Others here can amend this, if they know of an alternative.

>> >

>> > Thanks,

>> >

>> > Jen

>> >

>> > --

>> > Jennifer Hillman-Jackson

>> > Galaxy Application Support

>> > http://usegalaxy.org

>> > http://galaxyproject.org

>> > http://biostar.usegalaxy.org

>> >

>> >

>> > On Fri, Feb 26, 2016 at 4:01 AM, Makis Ladoukakis

>> > 

>> > wrote:

>> >

>> > Hello everyone,

>> >

>> > I was wondering whether it's possible to downgrade the upload tool to

>> > the

>> > previous version(1.1.4).

>> >

>> > I copied the upload.py and upload.xml scripts from a previous galaxy

>> > version

>> > to the tools/data_source/ directory and reloaded the tool as admin but

>> > it

>> > hasn't changed even when I restarted the server.

>> >

>> > Do I have to change