date:20160309

[galaxy-dev] Missing dependency issue

2016-03-09 Thread Scott Szakonyi

Hello all,

I'm having an issue with a missing dependency for readline 6.2. When I try
to install or repair, I get the following error message:

configure: error: in
`/vectorbase/web/Galaxy/galaxy/data/galaxy/tmp/tmp-toolshed-mtd3fhemK/readline-6.2':
configure: error: cannot compute suffix of object files: cannot compile
See `config.log' for more details.


I've tried to locate the config.log file without success, so this is all I
have to go on. Has anyone else encountered this sort of issue, and if so,
how did you solve it?

Thanks!

-- 
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] iRODS

2016-03-09 Thread Dan Bedard

The iRODS dev team is certainly interested in how people are using and want to 
use iRODS with Galaxy. Mikael, we would be happy to host the PDF and/or a guest 
blog post about making it work. And we can provide some assistance if there are 
difficulties on the iRODS side of this.

Cheers,
Dan Bedard

— 
Dan Bedard
Executive Director
iRODS Consortium

mobile: 1-919-346-3262
email: d...@renci.org
twitter: @DataDanB

iRODS User Group Meeting 2016
June 7-9 -- Chapel Hill, NC -- https://irods.org/ugm2016


> Message: 2
> Date: Wed, 9 Mar 2016 01:24:24 +
> From: "Kandalaft, Iyad" 
> To: James Taylor , Mohamed Kassam
>   
> Cc: "galaxy-dev@lists.galaxyproject.org"
>   
> Subject: Re: [galaxy-dev] iRODS
> Message-ID:
>   
> Content-Type: text/plain; charset="us-ascii"
> 
> We were considering implementing data pull/push tools for Galaxy-iRODS 
> integration but we haven't started work on that.
> I recall that the Galaxy team looked at backing Galaxy with iRODS but moved 
> away from the idea.  There was a trello card with that information.
> 
> 
> Iyad Kandalaft
> Bioinformatics Systems Developer
> Microbial Biodiversity Bioinformatics
> Science & Technology Branch
> Agriculture & Agri-Food Canada
> iyad.kandal...@agr.gc.ca | (613) 759-1228
> 
> 
> From: galaxy-dev [galaxy-dev-boun...@lists.galaxyproject.org] on behalf of 
> James Taylor [ja...@bx.psu.edu]
> Sent: March 8, 2016 10:09 AM
> To: Mohamed Kassam
> Cc: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] iRODS
> 
> Mohamed,
> 
> We implemented but never deployed the iRODS object store, so I suspect
> it has not been tested much. If anyone out there is using it please
> let us know.
> 
> On Mon, Mar 7, 2016 at 10:30 AM, Mohamed Kassam  wrote:
>> Dear all,
>> I would like to use our interlan iRODs to pull data.
>> I searched and i find that there is an object store for that.
>> How it works ? DO  I need to configure something else ?
>> 
>> Thanks in advance,
>> 
>> 
>> Mohamed
>> 
>> ___
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> 
> 
> --
> 
> Message: 3
> Date: Wed, 9 Mar 2016 12:01:38 +0100
> From: Mikael Loaec 
> To: galaxy-dev@lists.galaxyproject.org
> Cc: Olivier Inizan 
> Subject: [galaxy-dev] iRODS
> Message-ID: <56e00292.5070...@versailles.inra.fr>
> Content-Type: text/plain; charset=utf-8
> 
> Hi,
> 
> @URGI, we have sucessfully tested connexion of galaxy instance with an
> iRODS.
> We have a pdf doc 67ko) explaining how we implement it if you want, but
> don't  know if i can send attachement on this mailinglist ?
> 
> We (URGI) are also very interresting in data pull/push tools for
> Galaxy-iRODS integration. Let us know when you will begin working on it.
> 
> Regards,
> 
> Mikael LOAEC
> Systems and Networks Administrator
> URGI INRA
> 
> 
> --
> 
> Message: 4
> Date: Wed, 9 Mar 2016 12:43:36 +0100
> From: Mohamed Kassam 
> To: Mikael Loaec 
> Cc: galaxy-dev@lists.galaxyproject.org, Olivier Inizan
>   
> Subject: Re: [galaxy-dev] iRODS
> Message-ID:
>

Re: [galaxy-dev] quota api error

2016-03-09 Thread Dannon Baker

Fabien,

Thanks for the patch.  I've opened a PR applying it in
https://github.com/galaxyproject/galaxy/pull/1898.  I'm thinking we might
want to eventually refactor a little and add more general support for
Decimal serialization, perhaps in the 'safe_dumps' machinery in
galaxy.util.json, but this looks good to me for now.

On Tue, Mar 8, 2016 at 12:42 PM, Fabien Mareuil  wrote:

> Hi Dannon,
>
> I got this error with a detail view (/api/quotas/f597429621d6eb2b) when
> the quota has associated users with a disk usage different of 0,
> total_disk_usage in the user dictionary is a Decimal object and is not
> serializable.
> I worked on it this afternoon, it's possible to correct it just by adding
> the key 'total_disk_usage' in the value_mapper of the show method of
> QuotaAPIController class like the show method of UserAPIController class.
> I join a patch for the quota.py file with this email
> I can propose a pull request if you want.
>
>
> Best,
>
> --
> Fabien Mareuil | Centre d'Informatique pour la Biologie
> fabien.mare...@pasteur.fr | Institut Pasteur
> 25,28 rue du Docteur Roux 75015 Paris, France
>
>
>
> Le 08/03/2016 16:24, Dannon Baker a écrit :
>
> Hi Fabien,
>
> I'm having trouble reproducing this error on my side.  In the trace it
> looks like the error is being thrown at the collection view (/api/quotas)
> and not the detail view (/api/quotas/f597429621d6eb2b or the like).  Is
> that true?
>
> Can you show me the exact configuration of this quota in the admin panel?
>
> On Tue, Mar 8, 2016 at 8:10 AM, Fabien Mareuil 
> wrote:
>
>> Hi,
>>
>> We got an error when we used API to see a quota detail, we get the
>> following traceback:
>>
>> 157.99.60.167 - - [08/Mar/2016:10:13:58 +0200] "GET /api/quotas HTTP/1.1"
>> 200 - "-" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:44.0) Gecko/20100101
>> Firefox/44.0"
>> galaxy.web.framework.decorators ERROR 2016-03-08 10:14:10,273 Uncaught
>> exception in exposed API method:
>> Traceback (most recent call last):
>>   File ".../lib/galaxy/web/framework/decorators.py", line 142, in
>> decorator
>> rval = dumps( rval, indent=4, sort_keys=True )
>>   File ".../lib/galaxy/util/json.py", line 65, in safe_dumps
>> dumped = json.dumps( *args, allow_nan=False, **kwargs )
>>   File "/usr/lib64/python2.6/json/__init__.py", line 237, in dumps
>> **kw).encode(obj)
>>   File "/usr/lib64/python2.6/json/encoder.py", line 367, in encode
>> chunks = list(self.iterencode(o))
>>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
>> for chunk in self._iterencode_dict(o, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
>> _iterencode_dict
>> for chunk in self._iterencode(value, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 306, in _iterencode
>> for chunk in self._iterencode_list(o, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 204, in
>> _iterencode_list
>> for chunk in self._iterencode(value, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
>> for chunk in self._iterencode_dict(o, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
>> _iterencode_dict
>> for chunk in self._iterencode(value, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 309, in _iterencode
>> for chunk in self._iterencode_dict(o, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 275, in
>> _iterencode_dict
>> for chunk in self._iterencode(value, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 317, in _iterencode
>> for chunk in self._iterencode_default(o, markers):
>>   File "/usr/lib64/python2.6/json/encoder.py", line 323, in
>> _iterencode_default
>> newobj = self.default(o)
>>   File "/usr/lib64/python2.6/json/encoder.py", line 344, in default
>> raise TypeError(repr(o) + " is not JSON serializable")
>> TypeError: Decimal('856488698767') is not JSON serializable
>>
>> json can't serialize Decimal object.
>> I tested it with simplejson and it works.
>> An other solution is to convert the Decimal object to a float before the
>> dumps.
>>
>> Thanks a lot for your help
>> Best regards,
>>
>> --
>> Fabien Mareuil | Centre d'Informatique pour la Biologie
>> fabien.mare...@pasteur.fr | Institut Pasteur
>> 25,28 rue du Docteur Roux 75015 Paris, France
>>
>>
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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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Re: [galaxy-dev] iRODS

2016-03-09 Thread Will Holtz

Please consider posting the content of your doc to the Galaxy Community Log
Board , so that other people
can find it.

-Will

On Wed, Mar 9, 2016 at 3:01 AM, Mikael Loaec <
mikael.lo...@versailles.inra.fr> wrote:

> Hi,
>
> @URGI, we have sucessfully tested connexion of galaxy instance with an
> iRODS.
> We have a pdf doc 67ko) explaining how we implement it if you want, but
> don't  know if i can send attachement on this mailinglist ?
>
> We (URGI) are also very interresting in data pull/push tools for
> Galaxy-iRODS integration. Let us know when you will begin working on it.
>
> Regards,
>
> Mikael LOAEC
> Systems and Networks Administrator
> URGI INRA
> ___
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Re: [galaxy-dev] Setting job_working_directory on per-tool basis? (cuffdiff/cummerbund SQLite db error)

2016-03-09 Thread Peter Briggs


Just to follow up on my own questions, in case it's of interest to others:

-- Re specifying different job working directories on a per-tool basis:

Having spent a bit of time looking at the "advanced" sample job_conf.xml 
and also at the code for setting up and dispatching jobs, it looks to me 
like it is not possible to do this (i.e. specify different job working 
directories within different job destinations).


In fact as far as I can tell (I'm slightly lost within the Galaxy code 
at this point), it looks like the working directory is created within 
the job wrapper (via the objectstore interface) before the handler is 
assigned.


I'm wondering if a possible workaround might be to use Pulsar running on 
the same server, but it looks like a lot of overhead for my current 
problem (especially as I don't have any experience currently with using 
Pulsar).


-- Re cuffdiff cummeRbund SQLite database error:

It looks like changing the job_working_directory to a non-lustre 
filesystem fixes this problem.


Best wishes

Peter

On 08/03/16 09:37, Peter Briggs wrote:

Hello

I've encountered an issue with running the cuffdiff tool on our local
production Galaxy instance.

Specifically when a cummerbund SQLite database is requested as output
then the tool fails with an error:

Creating database ./cummeRbund.sqlite
Error in sqliteSendQuery(con, statement, bind.data) :
   error in statement: disk I/O error
Error in sqliteSendQuery(con, statement, bind.data) :
   error in statement: disk I/O error
Calls: readCufflinks ... .local -> sqliteGetQuery -> sqliteSendQuery ->
.Call
Execution halted

Our Galaxy is configured to use a LustreFS scratch directory for the
'job_working_directory', which I understand is where each job will have
its own working directory created, and I'm wondering if the SQLite error
above is a manifestation of a general problem with SQLite on LustreFS
(see e.g. the answer to this BioStars question
https://www.biostars.org/p/115452/).

The obvious workaround is to change 'job_working_directory', preferably
just for the cuffdiff tool. Does anyone know if it's possible to do this
i.e. set 'job_working_directory' on a per-tool basis?

(Also, has anyone else seen this specific problem with
cuffdiff/cummerbund/SQLite on their local Galaxy instances?)

Thanks for your help - any suggestions greatly appreciated,

Best wishes

Peter



--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: [galaxy-dev] Error installing from main toolshed

2016-03-09 Thread Dannon Baker

Hi Anmol,

It's a known temporary issue that we're working on right now.  Should be
resolved shortly.

-Dannon

On Wed, Mar 9, 2016 at 8:49 AM, Anmol Hemrom  wrote:

> Hi,
>
> I am getting error " HTTPError: HTTP Error 500: Internal Server Error"
> while installing tools from the main toolshed. I tried from different
> galaxy instances and got the same error.
>
> I have tried to export revision of a tool, that too threw the same error.
>
> Is it a temporary issue with main toolshed?  The testtoolshed is not
> working as well.
>
> Thanks
> Anmol
>
>
>
>
>
>
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Re: [galaxy-dev] iRODS

2016-03-09 Thread Mohamed Kassam

Thank you for your message,

I sent to you Mikael an email if you can semd your pdf.

It is a good idea to see if in The galaxy dev team they can integrate iRODS
for the next release.

Best regards,

Mohamed

2016-03-09 12:01 GMT+01:00 Mikael Loaec :

> Hi,
>
> @URGI, we have sucessfully tested connexion of galaxy instance with an
> iRODS.
> We have a pdf doc 67ko) explaining how we implement it if you want, but
> don't  know if i can send attachement on this mailinglist ?
>
> We (URGI) are also very interresting in data pull/push tools for
> Galaxy-iRODS integration. Let us know when you will begin working on it.
>
> Regards,
>
> Mikael LOAEC
> Systems and Networks Administrator
> URGI INRA
> ___
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[galaxy-dev] iRODS

2016-03-09 Thread Mikael Loaec

Hi,

@URGI, we have sucessfully tested connexion of galaxy instance with an
iRODS.
We have a pdf doc 67ko) explaining how we implement it if you want, but
don't  know if i can send attachement on this mailinglist ?

We (URGI) are also very interresting in data pull/push tools for
Galaxy-iRODS integration. Let us know when you will begin working on it.

Regards,

Mikael LOAEC
Systems and Networks Administrator
URGI INRA
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[galaxy-dev] Missing dependency issue

Re: [galaxy-dev] iRODS

Re: [galaxy-dev] quota api error

Re: [galaxy-dev] iRODS

Re: [galaxy-dev] Setting job_working_directory on per-tool basis? (cuffdiff/cummerbund SQLite db error)

Re: [galaxy-dev] Error installing from main toolshed

Re: [galaxy-dev] iRODS

[galaxy-dev] iRODS

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