Re: [galaxy-dev] Modifying a Cloud Cluster Instance

[Enis Afgan]

Give you seemingly have a custom deployment, a manual upgrade is probably
best. Instructions are available here:
https://wiki.galaxyproject.org/CloudMan/Services/Galaxy#Updating_Galaxy_source

We'll get the 16.07 release done too but juding by the way things look, it
won't be until the next month.

On Wed, Sep 14, 2016 at 11:23 AM, Lapointe, David 
wrote:

> Hi Enis,
>
> Yes I figured what I was doing wrong. Using Cloudman to restart services
> overwrote my confs.   Using the CLI to manage services keeps everything in
> place, though I would like to figure out what is the optimal way to move to
> 16.07. Wait for the AMI or update?
> --
> David Lapointe Ph.D.
> Sr. Bioinformatics Specialist
> Research Technology (RT)
> Tufts Technology Services (TTS)
> 16 Dearborn Road
> Somerville MA 02144
>
> Phone:  617-627-5319
> Fax: 617-627-3667
> http://it.tufts.edu
>
> From: Enis Afgan 
> Date: Wednesday, September 14, 2016 at 11:01 AM
> To: David Lapointe 
> Cc: "galaxy-dev@lists.galaxyproject.org"  galaxyproject.org>
> Subject: Re: [galaxy-dev] Modifying a Cloud Cluster Instance
>
> Hi David,
> I totally missed this email from you - apologies! Are you still trying to
> do this or did you figure it out? Following the general guidelines on
> customizing the instance is a good place to start. There is an option in
> CloudMan to turn on non-signed SSL (from the Admin page) but the steps
> performed may be useful in trying to do the same manually. I believe it's
> necessary to just update and reload the Nginx configuration. A template can
> be found here https://github.com/galaxyproject/cloudman/blob/
> 8db478a8d777bcc48ed8c838f1f9de8519a11e60/cm/conftemplates/
> nginx_server_ssl.default
>
> Hope this helps and, again, sorry for not getting back to you earlier.
>
>
> On Thu, Aug 11, 2016 at 2:30 PM, Lapointe, David  > wrote:
>
>> This is on Amazon I should add.
>> --
>> David Lapointe Ph.D.
>> Sr. Bioinformatics Specialist
>> Research Technology (RT)
>> Tufts Technology Services (TTS)
>> 16 Dearborn Road
>> Somerville MA 02144
>>
>> Phone:  617-627-5319
>> Fax: 617-627-3667
>> http://it.tufts.edu
>>
>> From: galaxy-dev  on behalf
>> of David Lapointe 
>> Date: Thursday, August 11, 2016 at 1:44 PM
>> To: "galaxy-dev@lists.galaxyproject.org" > t.org>
>> Subject: [galaxy-dev] Modifying a Cloud Cluster Instance
>>
>> I have  a Cloudman instance up and running, but I would like to add SSL (
>> I have a signed cert and key ) and productionize it.  I see several methods
>> documented,but it's not clear which one is preferred: edit in place then
>> persist changes and restart  (wiki/Cloudman/CustomizeGalaxyCloud) seems
>> best to me. Any advice?
>>
>> Thanks
>>
>> David
>> --
>> David Lapointe Ph.D.
>> Sr. Bioinformatics Specialist
>> Research Technology (RT)
>> Tufts Technology Services (TTS)
>> 16 Dearborn Road
>> Somerville MA 02144
>>
>> Phone:  617-627-5319
>> Fax: 617-627-3667
>> http://it.tufts.edu
>>
>> ___
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>>
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>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
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Re: [galaxy-dev] Authentication issue

[Nicola Soranzo]

Hi Mohamed,
- what Galaxy release are you using?
- what LDAP server are you using?
- how did you configured LDAP auth? remote user or using 
config/auth_conf.xml


Cheers,
Nicola

On 15/09/16 18:27, Mohamed Kassam wrote:

Dear all
I have an issue today, with authentication in our galaxy instance.
I restarted our instance and now new user can not be auto register 
automatically.
I am using the ldap of our institute, old user can login but when a new user 
wants to login it says user or email invalid however I saw on the terminal that 
ldap authentication is successful.

Do you know if someone had the some issue or problem with the the database.

Thanks in advance

Mohamed


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[galaxy-dev] Authentication issue

[Mohamed Kassam]

Dear all
I have an issue today, with authentication in our galaxy instance.
I restarted our instance and now new user can not be auto register 
automatically.
I am using the ldap of our institute, old user can login but when a new user 
wants to login it says user or email invalid however I saw on the terminal that 
ldap authentication is successful.

Do you know if someone had the some issue or problem with the the database.

Thanks in advance

Mohamed 


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Re: [galaxy-dev] Problem downloading HTML datasets

[Stephanie LE GRAS]

Thank you for your feedback ! It seems that we don’t have the problem anymore 
with our test instance (16.07)

Steph


De :  au nom de Cristel Thomas 
Date : mercredi 14 septembre 2016 14:20
À : Stephanie Le Gras 
Cc : "galaxy-dev@lists.galaxyproject.org" 
Objet : Re: [galaxy-dev] Problem downloading HTML datasets

Not that helpful, but we have the same problem with our 16.04 instance.

On Tue, Sep 13, 2016 at 10:21 AM, Stephanie LE GRAS 
> wrote:
Hi there,

I’m currently facing several problems with the galaxy instance I’m managing. 
I’m going to send a mail per problem so sorry in advance : for flooding !

The first problem I’m facing is that we can’t download HTML datasets from 
Galaxy. Here is the error I got when I try to do download an HTML dataset :

URL: http://use.galaxeast.fr/datasets/ff16fe18e3db62e7/display?to_ext=html
File 
'/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/weberror/evalexception.py',
 line 431 in respond
  app_iter = self.application(environ, detect_start_response)
File 
'/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/recursive.py',
 line 85 in __call__
  return self.application(environ, start_response)
File 
'/data2/galaxy/production/galaxy/.venv/lib/python2.7/site-packages/paste/httpexceptions.py',
 line 640 in __call__
  return self.application(environ, start_response)
File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 
131 in __call__
  return self.handle_request( environ, start_response )
File '/data2/galaxy/production/galaxy/lib/galaxy/web/framework/base.py', line 
190 in handle_request
  body = method( trans, **kwargs )
File 
'/data2/galaxy/production/galaxy/lib/galaxy/webapps/galaxy/controllers/dataset.py',
 line 245 in display
  return data.datatype.display_data(trans, data, preview, filename, to_ext, 
offset=offset, ck_size=ck_size, **kwd)
File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 353 
in display_data
  return self._archive_composite_dataset( trans, data, **kwd )
File '/data2/galaxy/production/galaxy/lib/galaxy/datatypes/data.py', line 235 
in _archive_composite_dataset
  params = util.Params( kwd )
File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 683 in 
__init__
  self.__dict__[ key ] = sanitize_param( value )
File '/data2/galaxy/production/galaxy/lib/galaxy/util/__init__.py', line 488 in 
sanitize_param
  raise Exception('Unknown parameter type (%s)' % ( type( value ) ))
Exception: Unknown parameter type ()

We don’t want to disable the sanitize process and we try to add some tools that 
generate HTML datasets into the whitelist but it didn’t solve our problem.

Version of Galaxy : release_16.04

Any idea about what the problem can be ?

Many thanks in advance for any help,

Best regards,

Stephanie

--
Stephanie Le Gras
INSERM
Computational scientist - Bioinformatician
GenomEast platform (former Microarray and Sequencing platform)
IGBMC
1, rue Laurent Fries
67404 ILLKIRCH Cedex
France
Tel. : +33 (0)3 88 65 32 73


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Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web browser

[Stephanie LE GRAS]

Dear Martin,

It’s worked for both.
I’ve just tried to log in using Safari private window and it didn’t work 
neither…

Steph


De : Martin Čech 
Date : mardi 13 septembre 2016 17:43
À : Stephanie Le Gras , "galaxy-dev@lists.galaxyproject.org" 

Objet : Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web 
browser

Stephanie:

can you log in to usegalaxy.org or 
test.galaxyproject.org using Safari? Also please 
try to login to your instance using Safari private window.

Martin

On Tue, Sep 13, 2016 at 11:33 AM Stephanie LE GRAS 
> wrote:
Hi Martin,

Thank you for your feedback. We don’t have any javascript errors…

Stephanie

De : Martin Čech >
Date : mardi 13 septembre 2016 16:36
À : Stephanie Le Gras >, 
"galaxy-dev@lists.galaxyproject.org" 
>
Objet : Re: [galaxy-dev] Can't log in to Galaxy instance using Safari web 
browser

Hello Stephanie,

I have just tested this on 16.07 and on `dev` branch of Galaxy and it works for 
both in my case. Can you please check the browser's console for javascript 
errors?

Thanks,

Martin
On Tue, Sep 13, 2016 at 10:22 AM Stephanie LE GRAS 
> wrote:
Hi there (again),

Another problem we are currently facing is that we cannot log in anymore on our 
galaxy instance using Safari. It’s working with Firefox and Chrome but when we 
are using Safari (with the right password and login) we just see a green box 
saying that we successfully logged in and we go back to the log in page.

This is a problem we are encountering on our test instance that we’ve just 
updated to the latest release release_16.07.

Any idea about what the problem can be ?

Many thanks in advance for any help,

Best regards,

Stephanie
--
Stephanie Le Gras
INSERM
Computational scientist - Bioinformatician
GenomEast platform (former Microarray and Sequencing platform)
IGBMC
1, rue Laurent Fries
67404 ILLKIRCH Cedex
France
Tel. : +33 (0)3 88 65 32 73

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