Re: [galaxy-dev] job_conf.xml and nativespecification

[Björn Grüning]

Hi Laure,

a hacky way it to use dynamic job destinations:

https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping

You can get the username via python and change "nativeSpecification" on
demand.

Hope this helps,
Bjoern

Am 14.09.2016 um 17:07 schrieb Laure QUINTRIC:
> Hi galaxy users,
> 
> while using galaxy with drmaa and real user on drm system, I would like
> to know if there's a way to set the variable PBS_O_LOGNAME to the real
> user name in the job_conf.xml :
> 
> -v PBS_O_LOGNAME=[REAL_USER_NAME??] -q
> test -l mem=100gb 
> 
> Thank you,
> 
> Laure
> 
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Re: [galaxy-dev] Modifying a Cloud Cluster Instance

[Lapointe, David]

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

[Enis Afgan]

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"  galaxyproject.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
>
> ___
> 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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[galaxy-dev] job_conf.xml and nativespecification

[Laure QUINTRIC]

Hi galaxy users,

while using galaxy with drmaa and real user on drm system, I would like 
to know if there's a way to set the variable PBS_O_LOGNAME to the real 
user name in the job_conf.xml :


-v PBS_O_LOGNAME=[REAL_USER_NAME??] -q 
test -l mem=100gb 


Thank you,

Laure

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[galaxy-dev] multiqc

[Jochen Bick]

Hi,

I'm having trouble installing multiqc, this is the current error message:

Traceback (most recent call last):
  File "setup.py", line 32, in 
""".format(version))
ValueError: zero length field name in format


interestingly I could install it on our developer instance which runs on
16.01 and not on your production instance 15.10.

Any suggestions?

Thanks Jochen



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Re: [galaxy-dev] Problem downloading HTML datasets

[Cristel Thomas]

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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>
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Re: [galaxy-dev] Odd error, solution not understood

[Scott Szakonyi]

Ah, thank you very much, Hans-Rudolf. That did the trick.

Best regards,

Scott

On Wed, Sep 14, 2016 at 6:56 AM, Hans-Rudolf Hotz  wrote:

> Hi Scott
>
> click on the question mark next to 'database' in your history item and set
> the "Database/Build" to the genome you need.
>
>
> Regards, Hans-Rudolf
>
> On 09/13/2016 09:11 PM, Scott Szakonyi wrote:
>
>> Hi all,
>>
>> I'm getting the following error when attempting to do a trackster
>> visualization:
>>
>> Error: The requested genome file (/vectorbase/web/Galaxy/galaxy
>> /tool-data/shared/ucsc/chrom/?.len) could not be opened. Exiting!
>> Couldn't open /vectorbase/web/Galaxy/galaxy/
>> tool-data/shared/ucsc/chrom/?.len
>>
>> I found a discussion related to this error online at
>> https://biostar.usegalaxy.org/p/6938/, but I'm unsure what the offered
>> solution actually means in terms of what I need to do. It says "
>> You'll need to set your dataset's database/dbkey to your custom
>> reference genome before you can visualize it". Can someone point me in
>> the right direction to solve this issue?
>>
>> Thanks in advance,
>>
>> 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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>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>https://lists.galaxyproject.org/
>>
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>>http://galaxyproject.org/search/mailinglists/
>>
>>


-- 
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] Odd error, solution not understood

[Hans-Rudolf Hotz]

Hi Scott

click on the question mark next to 'database' in your history item and 
set the "Database/Build" to the genome you need.



Regards, Hans-Rudolf

On 09/13/2016 09:11 PM, Scott Szakonyi wrote:

Hi all,

I'm getting the following error when attempting to do a trackster
visualization:

Error: The requested genome file 
(/vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len) could not be 
opened. Exiting!
Couldn't open 
/vectorbase/web/Galaxy/galaxy/tool-data/shared/ucsc/chrom/?.len

I found a discussion related to this error online at
https://biostar.usegalaxy.org/p/6938/, but I'm unsure what the offered
solution actually means in terms of what I need to do. It says "
You'll need to set your dataset's database/dbkey to your custom
reference genome before you can visualize it". Can someone point me in
the right direction to solve this issue?

Thanks in advance,

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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